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Lutz Í, Martins T, Santana P, Ferreira C, Miranda J, Matos S, Muhala V, Sampaio I, Vallinoto M, Evangelista-Gomes G. Marine catfishes (Ariidae-Siluriformes) from the Coastal Amazon: mitochondrial DNA barcode for a recent diversification group? PeerJ 2024; 12:e17581. [PMID: 39221281 PMCID: PMC11365480 DOI: 10.7717/peerj.17581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 05/25/2024] [Indexed: 09/04/2024] Open
Abstract
Background Ariidae species play a significant role as fishing resources in the Amazon region. However, the family's systematic classification is notably challenging, particularly regarding species delimitation within certain genera. This difficulty arises from pronounced morphological similarities among species, posing obstacles to accurate species recognition. Methods Following morphological identification, mitochondrial markers (COI and Cytb) were employed to assess the diversity of Ariidae species in the Amazon. Results Our sampling efforts yielded 12 species, representing 92% of the coastal Amazon region's diversity. Morphological identification findings were largely corroborated by molecular data, particularly for species within the Sciades and Bagre genera. Nonetheless, despite morphological support, Cathorops agassizii and Cathorops spixii displayed minimal genetic divergence (0.010). Similarly, Notarius quadriscutis and Notarius phrygiatus formed a single clade with no genetic divergence, indicating mitochondrial introgression. For the majority of taxa examined, both COI and Cytb demonstrated efficacy as DNA barcodes, with Cytb exhibiting greater polymorphism and resolution. Consequently, the molecular tools utilized proved highly effective for species discrimination and identification.
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Affiliation(s)
- Ítalo Lutz
- Laboratório de Genética Aplicada (LAGA), Instituto de Estudos Costeiros (IECOS), Universidade Federal do Pará, Bragança, Brazil
| | - Thais Martins
- Laboratório de Genética Aplicada (LAGA), Instituto de Estudos Costeiros (IECOS), Universidade Federal do Pará, Bragança, Brazil
| | - Paula Santana
- Laboratório de Genética Aplicada (LAGA), Instituto de Estudos Costeiros (IECOS), Universidade Federal do Pará, Bragança, Brazil
| | - Charles Ferreira
- Laboratório de Genética Aplicada (LAGA), Instituto de Estudos Costeiros (IECOS), Universidade Federal do Pará, Bragança, Brazil
| | - Josy Miranda
- Laboratório de Genética Aplicada (LAGA), Instituto de Estudos Costeiros (IECOS), Universidade Federal do Pará, Bragança, Brazil
| | - Suane Matos
- Laboratório de Genética Aplicada (LAGA), Instituto de Estudos Costeiros (IECOS), Universidade Federal do Pará, Bragança, Brazil
| | - Valdemiro Muhala
- Divisão de Agricultura, Instituto Superior Politécnico de Gaza, Chókwè, Mozambique
- Laboratório de Evolução (LEVO), Instituto de Estudos Costeiros (IECOS), Universidade Federal do Pará, Bragança, Brazil
| | - Iracilda Sampaio
- Laboratório de Evolução (LEVO), Instituto de Estudos Costeiros (IECOS), Universidade Federal do Pará, Bragança, Brazil
| | - Marcelo Vallinoto
- Laboratório de Evolução (LEVO), Instituto de Estudos Costeiros (IECOS), Universidade Federal do Pará, Bragança, Brazil
| | - Grazielle Evangelista-Gomes
- Laboratório de Genética Aplicada (LAGA), Instituto de Estudos Costeiros (IECOS), Universidade Federal do Pará, Bragança, Brazil
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2
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Baxter JR, Kotze A, de Bruyn M, Matlou K, Labuschagne K, Mwale M. DNA barcoding of southern African mammal species and construction of a reference library for forensic application. Genome 2024. [PMID: 38996389 DOI: 10.1139/gen-2023-0050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2024]
Abstract
Combating wildlife crimes in South Africa requires accurate identification of traded species and their products. Diagnostic morphological characteristics needed to identify species are often lost when specimens are processed and customs officials lack the expertise to identify species. As a potential solution, DNA barcoding can be used to identify morphologically indistinguishable specimens in forensic cases. However, barcoding is hindered by the reliance on comprehensive, validated DNA barcode reference databases, which are currently limited. To overcome this limitation, we constructed a barcode library of cytochrome c oxidase subunit 1 and cytochrome b sequences for threatened and protected mammals exploited in southern Africa. Additionally, we included closely related or morphologically similar species and assessed the database's ability to identify species accurately. Published southern African sequences were incorporated to estimate intraspecific and interspecific variation. Neighbor-joining trees successfully discriminated 94%-95% of the taxa. However, some widespread species exhibited high intraspecific distances (>2%), suggesting geographic sub-structuring or cryptic speciation. Lack of reliable published data prevented the unambiguous discrimination of certain species. This study highlights the efficacy of DNA barcoding in species identification, particularly for forensic applications. It also highlights the need for a taxonomic re-evaluation of certain widespread species and challenging genera.
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Affiliation(s)
- J R Baxter
- South African National Biodiversity Institute, PO BOX 754, Pretoria 0001, South Africa
| | - A Kotze
- South African National Biodiversity Institute, PO BOX 754, Pretoria 0001, South Africa
- Department of Genetics, Faculty of Natural and Agricultural Sciences, University of the Free State, PO Box 339, Bloemfontein 9300, South Africa
| | - M de Bruyn
- South African National Biodiversity Institute, PO BOX 754, Pretoria 0001, South Africa
| | - K Matlou
- South African National Biodiversity Institute, PO BOX 754, Pretoria 0001, South Africa
| | - K Labuschagne
- South African National Biodiversity Institute, PO BOX 754, Pretoria 0001, South Africa
| | - M Mwale
- South African National Biodiversity Institute, PO BOX 754, Pretoria 0001, South Africa
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3
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Bañón R, Barros-García D, Baldó F, Cojan M, de Carlos A. Unveiling taxonomic diversity in the deep-sea fish genus Notacanthus (Notacanthiformes: Notacanthidae) with description of Notacanthus arrontei n. sp. JOURNAL OF FISH BIOLOGY 2024; 104:1910-1923. [PMID: 38513288 DOI: 10.1111/jfb.15734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 02/27/2024] [Accepted: 03/05/2024] [Indexed: 03/23/2024]
Abstract
Notacanthid fishes constitute a common part of benthopelagic deep-sea fish communities on seamounts and continental slopes around the world. However, their highly conserved morphology and the usual lack of information on deep-water organisms make it difficult to appropriately address their biodiversity. A multidisciplinary approach combining morphological data with a DNA-based species delimitation analyses was used to explore the taxonomy of Notacanthus species. For this purpose, morphological and molecular data were obtained from 43 individuals, and the resulting information was combined with the available data. The results showed the occurrence of Notacanthus arrontei n. sp. from the Iberian Peninsula and highlighted several taxonomic conundrums regarding the Notacanthus genus. For instance, no significant differences were found between Notacanthus indicus and the recently described Notacanthus laccadiviensis, questioning its taxonomic status. Similarly, the result of the species delimitation molecular analysis coincided with previous DNA barcoding studies supporting the snubnosed spiny eel Notacanthus chemnitzii as a species complex that requires further research. Moreover, two unidentified records from the Indian Ocean were confirmed to belong to an unknown species pending formal description, and barcoding data show for the first time the occurrence of the shortfin spiny eel Notacanthus bonaparte in the Australia-New Zealand area. This research confirms the existence of important gaps in the knowledge of notacanthid fishes and represents a step forward toward a better understanding of their biological diversity.
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Affiliation(s)
- Rafael Bañón
- Grupo de Estudo do Medio Mariño (GEMM), Ribeira, Spain
| | - David Barros-García
- Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR/CIMAR), Matosinhos, Portugal
| | - Francisco Baldó
- Centro Oceanográfico de Cádiz, Instituto Español de Oceanografía, Consejo Superior de Investigaciones Científicas, Cádiz, Spain
| | - Miguel Cojan
- Centro Oceanográfico de Cádiz, Instituto Español de Oceanografía, Consejo Superior de Investigaciones Científicas, Cádiz, Spain
| | - Alejandro de Carlos
- Departamento de Bioquímica, Xenética e Inmunoloxía, Facultade de Bioloxía, Universidade de Vigo, Vigo, Spain
- Centro de Investigación Mariña da Universidade de Vigo (CIM-UVIGO), Vigo, Spain
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4
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Muhala V, Guimarães-Costa A, Macate IE, Rabelo LP, Bessa-Silva AR, Watanabe L, dos Santos GD, Sambora L, Vallinoto M, Sampaio I. DNA barcoding for the assessment of marine and coastal fish diversity from the Coast of Mozambique. PLoS One 2024; 19:e0293345. [PMID: 38319915 PMCID: PMC10846724 DOI: 10.1371/journal.pone.0293345] [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: 05/01/2023] [Accepted: 10/10/2023] [Indexed: 02/08/2024] Open
Abstract
The ichthyological provinces of Mozambique are understudied hotspots of global fish diversity. In this study, we applied DNA barcoding to identify the composition of the fish fauna from the coast of Mozambique. A total of 143 species belonging to 104 genera, 59 families, and 30 orders were identified. The overall K2P distance of the COI sequences within species ranged from 0.00% to 1.51%, while interspecific distances ranged from 3.64% to 24.49%. Moreover, the study revealed 15 threatened species according to the IUCN Red List of Threatened Species, with elasmobranchs being the most represented group. Additionally, the study also uncovered four new species that were not previously recorded in this geographic area, including Boleophthalmus dussumieri, Maculabatis gerrardi, Hippocampus kelloggi, and Lethrinus miniatus. This study represents the first instance of utilizing molecular references to explore the fish fauna along the Mozambican coast. Our results indicate that DNA barcoding is a dependable technique for the identification and delineation of fish species in the waters of Mozambique. The DNA barcoding library established in this research will be an invaluable asset for advancing the understanding of fish diversity and guiding future conservation initiatives.
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Affiliation(s)
- Valdemiro Muhala
- Laboratório de Evolução, Universidade Federal do Pará, Alameda Leandro Ribeiro, Aldeia, Bragança, Pará, Brazil
- Divisão de Agricultura, Instituto Superior Politécnico de Gaza, Chókwè, Mozambique
| | - Aurycéia Guimarães-Costa
- Laboratório de Evolução, Universidade Federal do Pará, Alameda Leandro Ribeiro, Aldeia, Bragança, Pará, Brazil
| | - Isadola Eusébio Macate
- Laboratório de Evolução, Universidade Federal do Pará, Alameda Leandro Ribeiro, Aldeia, Bragança, Pará, Brazil
- Departamento de Ciências Agrárias e Ambientais, Universidade Estadual de Santa Cruz, Ilheus, BA, Brazil
| | - Luan Pinto Rabelo
- Laboratório de Evolução, Universidade Federal do Pará, Alameda Leandro Ribeiro, Aldeia, Bragança, Pará, Brazil
| | - Adam Rick Bessa-Silva
- Laboratório de Evolução, Universidade Federal do Pará, Alameda Leandro Ribeiro, Aldeia, Bragança, Pará, Brazil
| | - Luciana Watanabe
- Laboratório de Evolução, Universidade Federal do Pará, Alameda Leandro Ribeiro, Aldeia, Bragança, Pará, Brazil
| | - Gisele Damasceno dos Santos
- Laboratório de Evolução, Universidade Federal do Pará, Alameda Leandro Ribeiro, Aldeia, Bragança, Pará, Brazil
| | - Luísa Sambora
- Departamento de Produção Agrária, Escola Superior de Desenvolvimento Rural, Universidade Eduardo Mondlane, Vilankulos, Moçambique
| | - Marcelo Vallinoto
- Laboratório de Evolução, Universidade Federal do Pará, Alameda Leandro Ribeiro, Aldeia, Bragança, Pará, Brazil
| | - Iracilda Sampaio
- Laboratório de Evolução, Universidade Federal do Pará, Alameda Leandro Ribeiro, Aldeia, Bragança, Pará, Brazil
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5
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Rossel S, Peters J, Charzinski N, Eichsteller A, Laakmann S, Neumann H, Martínez Arbizu P. A universal tool for marine metazoan species identification: towards best practices in proteomic fingerprinting. Sci Rep 2024; 14:1280. [PMID: 38218969 PMCID: PMC10787734 DOI: 10.1038/s41598-024-51235-z] [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: 08/30/2023] [Accepted: 01/02/2024] [Indexed: 01/15/2024] Open
Abstract
Proteomic fingerprinting using MALDI-TOF mass spectrometry is a well-established tool for identifying microorganisms and has shown promising results for identification of animal species, particularly disease vectors and marine organisms. And thus can be a vital tool for biodiversity assessments in ecological studies. However, few studies have tested species identification across different orders and classes. In this study, we collected data from 1246 specimens and 198 species to test species identification in a diverse dataset. We also evaluated different specimen preparation and data processing approaches for machine learning and developed a workflow to optimize classification using random forest. Our results showed high success rates of over 90%, but we also found that the size of the reference library affects classification error. Additionally, we demonstrated the ability of the method to differentiate marine cryptic-species complexes and to distinguish sexes within species.
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Affiliation(s)
- Sven Rossel
- Senckenberg am Meer, German Centre for Marine Biodiversity Research (DZMB), 26382, Wilhelmshaven, Germany.
| | - Janna Peters
- German Centre for Marine Biodiversity Research (DZMB), Senckenberg am Meer, 20146, Hamburg, Germany
| | - Nele Charzinski
- Marine Biodiversity Research, Institute of Biology and Environmental Sciences, Carl von Ossietzky University Oldenburg, 26129, Oldenburg, Germany
| | - Angelina Eichsteller
- Senckenberg am Meer, German Centre for Marine Biodiversity Research (DZMB), 26382, Wilhelmshaven, Germany
- Marine Biodiversity Research, Institute of Biology and Environmental Sciences, Carl von Ossietzky University Oldenburg, 26129, Oldenburg, Germany
| | - Silke Laakmann
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), 26129, Oldenburg, Germany
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Am Handelshafen 12, 27570, Bremerhaven, Germany
| | - Hermann Neumann
- Institute for Sea Fisheries, Thuenen Institute, 27572, Bremerhaven, Germany
| | - Pedro Martínez Arbizu
- Senckenberg am Meer, German Centre for Marine Biodiversity Research (DZMB), 26382, Wilhelmshaven, Germany
- Marine Biodiversity Research, Institute of Biology and Environmental Sciences, Carl von Ossietzky University Oldenburg, 26129, Oldenburg, Germany
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6
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Garbett A, Loca SL, Barreau T, Biscoito M, Bradley C, Breen J, Clarke M, Ellis JR, Griffiths AM, Hannon G, Jakobsdóttir K, Junge C, Lynghammar A, McCloskey M, Minos G, Phillips ND, Prodöhl PA, Roche W, Iglésias SP, Thorburn J, Collins PC. A holistic and comprehensive data approach validates the distribution of the critically endangered flapper skate (Dipturus intermedius). JOURNAL OF FISH BIOLOGY 2023; 103:516-528. [PMID: 37246738 DOI: 10.1111/jfb.15466] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 05/24/2023] [Indexed: 05/30/2023]
Abstract
Morphological similarities between skates of the genus Dipturus in the north-eastern Atlantic and Mediterranean have resulted in longstanding confusion, misidentification and misreporting. Current evidence indicates that the common skate is best explained as two species, the flapper skate (Dipturus intermedius) and the common blue skate (D. batis). However, some management and conservation initiatives developed prior to the separation continue to refer to common skate (as 'D. batis'). This taxonomic uncertainty can lead to errors in estimating population viability, distribution range, and impact on fisheries management and conservation status. Here, we demonstrate how a concerted taxonomic approach, using molecular data and a combination of survey, angler and fisheries data, in addition to expert witness statements, can be used to build a higher resolution picture of the current distribution of D. intermedius. Collated data indicate that flapper skate has a more constrained distribution compared to the perceived distribution of the 'common skate', with most observations recorded from Norway and the western and northern seaboards of Ireland and Scotland, with occasional specimens from Portugal and the Azores. Overall, the revised spatial distribution of D. intermedius has significantly reduced the extant range of the species, indicating a possibly fragmented distribution range.
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Affiliation(s)
- Amy Garbett
- Queen's University Marine Laboratory, Newtownards, UK
| | - Sophie L Loca
- Queen's University Marine Laboratory, Newtownards, UK
| | | | - Manuel Biscoito
- Funchal Natural History Museum, Funchal, Portugal
- Observatório Oceânico da Madeira, Funchal, Portugal
| | - Caroline Bradley
- Queen's University Belfast, School of Biological Sciences, Belfast, UK
| | - Joe Breen
- The Department of Agriculture, Environment and Rural Affairs (DAERA), Belfast, UK
| | | | - Jim R Ellis
- Centre for Environment, Fisheries and Aquaculture Science, Lowestoft, UK
| | | | - Gary Hannon
- Sea-Fisheries Protection Authority, National Seafood Centre, Clonakilty, Ireland
| | | | - Claudia Junge
- Havforskningsinstituttet (Institute of Marine Research), Stakkevollan, Tromsø, Norway
| | | | | | - George Minos
- International Hellenic University, Thessaloniki, Greece
| | | | - Paulo A Prodöhl
- Queen's University Belfast, School of Biological Sciences, Belfast, UK
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7
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Bourret A, Nozères C, Parent E, Parent GJ. Maximizing the reliability and the number of species assignments in metabarcoding studies using a curated regional library and a public repository. METABARCODING AND METAGENOMICS 2023. [DOI: 10.3897/mbmg.7.98539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023] Open
Abstract
Biodiversity assessments relying on DNA have increased rapidly over the last decade. However, the reliability of taxonomic assignments in metabarcoding studies is variable and affected by the reference databases and the assignment methods used. Species level assignments are usually considered as reliable using regional libraries but unreliable using public repositories. In this study, we aimed to test this assumption for metazoan species detected in the Gulf of St. Lawrence in the Northwest Atlantic. We first created a regional library (GSL-rl) by data mining COI barcode sequences from BOLD, and included a reliability ranking system for species assignments. We then estimated 1) the accuracy and precision of the public repository NCBI-nt for species assignments using sequences from the regional library and 2) compared the detection and reliability of species assignments of a metabarcoding dataset using either NCBI-nt or the regional library and popular assignment methods. With NCBI-nt and sequences from the regional library, the BLAST-LCA (least common ancestor) method was the most precise method for species assignments, but the accuracy was higher with the BLAST-TopHit method (>80% over all taxa, between 70% and 90% amongst taxonomic groups). With the metabarcoding dataset, the reliability of species assignments was greater using GSL-rl compared to NCBI-nt. However, we also observed that the total number of reliable species assignments could be maximized using both GSL-rl and NCBI-nt with different optimized assignment methods. The use of a two-step approach for species assignments, i.e., using a regional library and a public repository, could improve the reliability and the number of detected species in metabarcoding studies.
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8
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Awas M, Ahmed I, Ahmad SM, Al-Anazi KM, Farah MA, Bhat B. Integrative approach for validation of six important fish species inhabiting River Poonch of north-west Himalayan region (India). Front Genet 2023; 13:1047436. [PMID: 36726718 PMCID: PMC9886096 DOI: 10.3389/fgene.2022.1047436] [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: 09/18/2022] [Accepted: 11/29/2022] [Indexed: 01/06/2023] Open
Abstract
Traditionally, species of fish are identified based on morphological characteristics. Although these taxonomic descriptions are essential, there are cases where the morphological characters distinguishing these species show marginal differences. For instance, in the Poonch River in the Himalayas, there are 21 species, out of which some are morphologically similar, and the taxonomic distinction between these species is unclear. Therefore, in this study, we used sequences from two mitochondrial genes, Cytochrome b (Cyt b) and a larger ribosomal subunit (16S rRNA), as well as the morphological analysis to address any taxonomic ambiguities among the six fish species. Maximum Likelihood results revealed that all the species were clustered according to their families and genera. The phenotypic analysis also supported this statement, as all the species of different genera like Schizothorax, Tor, Garra, Traqilabeo, and Glyptothorax are grouped in their particular cluster, it shows that species of a separate class share a mutual morphological characteristic. While genetic analyses of these species suggest nucleotide diversity (p) and haplotype diversity, with Hd values as 0.644 for Cyt b and 0.899 for 16S rRNA, confirming the rich genetic diversity in the river. Overall, we recommend that the integrative approach in delimiting the fish species is more effective than the individual one and can be used to rapidly diagnose a species and understand the evolutionary relationship between the species.
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Affiliation(s)
- Mohd Awas
- Fish Nutrition Laboratory, Department of Zoology, University of Kashmir, Srinagar, India
| | - Imtiaz Ahmed
- Fish Nutrition Laboratory, Department of Zoology, University of Kashmir, Srinagar, India,*Correspondence: Imtiaz Ahmed, ; Syed Mudasir Ahmad,
| | - Syed Mudasir Ahmad
- Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, Sher-e-Kashmir University of Agricultural Sciences and Technology, Srinagar, India,*Correspondence: Imtiaz Ahmed, ; Syed Mudasir Ahmad,
| | | | - Mohammad Abul Farah
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Basharat Bhat
- Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, Sher-e-Kashmir University of Agricultural Sciences and Technology, Srinagar, India
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9
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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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10
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Collins RA, Trauzzi G, Maltby KM, Gibson TI, Ratcliffe FC, Hallam J, Rainbird S, Maclaine J, Henderson PA, Sims DW, Mariani S, Genner MJ. Meta-Fish-Lib: A generalised, dynamic DNA reference library pipeline for metabarcoding of fishes. JOURNAL OF FISH BIOLOGY 2021; 99:1446-1454. [PMID: 34269417 DOI: 10.1111/jfb.14852] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 07/06/2021] [Accepted: 07/12/2021] [Indexed: 06/13/2023]
Abstract
The accuracy and reliability of DNA metabarcoding analyses depend on the breadth and quality of the reference libraries that underpin them. However, there are limited options available to obtain and curate the huge volumes of sequence data that are available on public repositories such as NCBI and BOLD. Here, we provide a pipeline to download, clean and annotate mitochondrial DNA sequence data for a given list of fish species. Features of this pipeline include (a) support for multiple metabarcode markers; (b) searches on species synonyms and taxonomic name validation; (c) phylogeny assisted quality control for identification and removal of misannotated sequences; (d) automatically generated coverage reports for each new GenBank release update; and (e) citable, versioned DOIs. As an example we provide a ready-to-use curated reference library for the marine and freshwater fishes of the U.K. To augment this reference library for environmental DNA metabarcoding specifically, we generated 241 new MiFish-12S sequences for 88 U.K. marine species, and make available new primer sets useful for sequencing these. This brings the coverage of common U.K. species for the MiFish-12S fragment to 93%, opening new avenues for scaling up fish metabarcoding across wide spatial gradients. The Meta-Fish-Lib reference library and pipeline is hosted at https://github.com/genner-lab/meta-fish-lib.
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Affiliation(s)
- Rupert A Collins
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Giulia Trauzzi
- School of Biological Sciences, University of Bristol, Bristol, UK
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Katherine M Maltby
- Centre for Environment, Fisheries and Aquaculture Science, Lowestoft, UK
| | - Thomas I Gibson
- Molecular Ecology and Fisheries Genetics Laboratory, Bangor University School of Natural Sciences, Environment Centre Wales, Bangor, UK
| | | | - Jane Hallam
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Sophie Rainbird
- Marine Biological Association of the United Kingdom, Plymouth, UK
| | - James Maclaine
- Department of Life Sciences, The Natural History Museum, London, UK
| | | | - David W Sims
- Marine Biological Association of the United Kingdom, Plymouth, UK
- Ocean and Earth Science, University of Southampton, National Oceanography Centre Southampton, Southampton, UK
| | - Stefano Mariani
- Ecosystems & Environment Research Centre, School of Environment & Life Sciences, University of Salford, Salford, UK
- School of Biological & Environmental Sciences, Liverpool John Moores University, Liverpool, UK
| | - Martin J Genner
- School of Biological Sciences, University of Bristol, Bristol, UK
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11
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Lin X, Jiang K, Liu W, Liu W, Bu W, Wang X, Mo L. Toward a global DNA barcode reference library of the intolerant nonbiting midge genus Rheocricotopus Brundin, 1956. Ecol Evol 2021; 11:12161-12172. [PMID: 34522368 PMCID: PMC8427567 DOI: 10.1002/ece3.7979] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 07/16/2021] [Accepted: 07/19/2021] [Indexed: 01/01/2023] Open
Abstract
Environmental DNA metabarcoding is becoming a predominant tool in biodiversity assessment, as this time- and cost-efficient tactics have the ability to increase monitoring accuracy. As a worldwide distributed genus, Rheocricotopus Brundin, 1956 still does not possess a complete and comprehensive global DNA barcode reference library for biodiversity monitoring. In the present study, we compiled a cytochrome c oxidase subunit 1 (COI) DNA barcode library of Rheocricotopus with 434 barcodes around the world, including 121 newly generated DNA barcodes of 32 morphospecies and 313 public barcodes. Automatic Barcode Gap Discovery (ABGD) was applied on the 434 COI barcodes to provide a comparison between the operational taxonomic units (OTU) number calculated from the Barcode Index Number (BIN) with the "Barcode Gap Analysis" and neighbor-joining (NJ) tree analysis. Consequently, these 434 COI barcodes were clustered into 78 BINs, including 42 new BINs. ABGD yielded 51 OTUs with a prior intraspecific divergence of Pmax = 7.17%, while NJ tree revealed 52 well-separated clades. Conservatively, 14 unknown species and one potential synonym were uncovered with reference to COI DNA barcodes. Besides, based on our ecological analysis, we discovered that annual mean temperature and annual precipitation could be considered as key factors associated with distribution of certain members from this genus. Our global DNA barcode reference library of Rheocricotopus provides one fundamental database for accurate species delimitation in Chironomidae taxonomy and facilitates the biodiversity monitoring of aquatic biota.
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Affiliation(s)
- Xiao‐Long Lin
- College of Life SciencesNankai UniversityTianjinChina
| | - Kun Jiang
- College of Life SciencesNankai UniversityTianjinChina
| | - Wen‐Bin Liu
- Tianjin Key Laboratory of Conservation and Utilization of Animal DiversityTianjin Normal UniversityTianjinChina
| | - Wei Liu
- College of Life SciencesNankai UniversityTianjinChina
| | - Wen‐Jun Bu
- College of Life SciencesNankai UniversityTianjinChina
| | - Xin‐Hua Wang
- College of Life SciencesNankai UniversityTianjinChina
| | - Lidong Mo
- Crowther LabInstitute of Integrative BiologyETH Zurich (Swiss Federal Institute of Technology)ZurichSwitzerland
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12
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Madeira S, Duarte A, Boinas F, Costa Osório H. A DNA barcode reference library of Portuguese mosquitoes. Zoonoses Public Health 2021; 68:926-936. [PMID: 34398521 DOI: 10.1111/zph.12885] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 07/25/2021] [Accepted: 07/29/2021] [Indexed: 11/28/2022]
Abstract
Mosquitoes are important biological vectors of pathogens and species identification in all life stages is the first step for effective monitoring and control of mosquito-borne diseases. Molecular methods for species identification have been developed over the last years to overcome the limitations of the taxonomic identification based on morphology. DNA barcoding, using a fragment of the mitochondrial cytochrome oxidase I (COI) gene, can be used for species identification but a reliable and comprehensive reference database of verified sequences is required. In this study, we aimed to generate a DNA barcode reference library for the identification of mosquito species from Portuguese mosquito fauna, including most relevant vector species. Mosquitoes captured under the National Vector Surveillance Program (REVIVE) were processed for DNA extraction, COI gene fragment amplification and sequencing. Nighty-eight barcode sequences were obtained, representing 26 species and 6 genera. Sequences were submitted to GenBank and BOLD and were used for validation of phenetic classification. Barcode Index Number (BIN) assignment and Automatic Barcode Gap Discovery (ABGD) were used and clustered COI sequences into twenty-five molecular operational taxonomic units (MOTUs). This is the first comprehensive study that combines morphological and molecular identification of most mosquito species present in Portugal aiming to offer a reliable framework for mosquito species identification.
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Affiliation(s)
- Sara Madeira
- CIISA - Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, Lisboa, Portugal
| | - Ana Duarte
- CIISA - Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, Lisboa, Portugal
| | - Fernando Boinas
- CIISA - Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, Lisboa, Portugal
| | - Hugo Costa Osório
- Centro de Estudos de Vetores e Doenças Infeciosas Dr. Francisco Cambournac (CEVDI), Instituto Nacional de Saúde Doutor Ricardo Jorge (INSA), Águas de Moura, Portugal.,Instituto de Saúde Ambiental, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
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13
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Ahmed MS, Datta SK, Saha T, Hossain Z. Molecular characterization of marine and coastal fishes of Bangladesh through DNA barcodes. Ecol Evol 2021; 11:3696-3709. [PMID: 33976769 PMCID: PMC8093680 DOI: 10.1002/ece3.7355] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 01/31/2021] [Accepted: 02/03/2021] [Indexed: 12/02/2022] Open
Abstract
This study describes the molecular characterization of marine and coastal fishes of Bangladesh based on the mitochondrial cytochrome c oxidase subunit I (COI) gene as a marker. A total of 376 mitochondrial COI barcode sequences were obtained from 185 species belonging to 146 genera, 74 families, 21 orders, and two classes of fishes. The mean length of the sequences was 652 base pairs. In Elasmobranchii (Sharks and rays), the average Kimura two parameter (K2P) distances within species, genera, families, and orders were 1.20%, 6.07%, 11.08%, and 14.68%, respectively, and for Actinopterygii, the average K2P distances within species, genera, families, and orders were 0.40%, 6.36%, 14.10%, and 24.07%, respectively. The mean interspecies distance was 16-fold higher than the mean intraspecies distance. The K2P neighbor-joining (NJ) trees based on the sequences generally clustered species in accordance with their taxonomic position. A total of 21 species were newly recorded in Bangladesh. High efficiency and fidelity in species identification and discrimination were demonstrated in the present study by DNA barcoding, and we conclude that COI sequencing can be used as an authentic identification marker for Bangladesh marine fish species.
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Affiliation(s)
| | | | - Tonmoy Saha
- Department of ZoologyJagannath UniversityDhakaBangladesh
| | - Zarif Hossain
- Department of OceanographyUniversity of DhakaDhakaBangladesh
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14
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DNA barcoding for identification of fishes in Xiangjiaba reservoir area in the downstream section of the Jinsha river. CONSERV GENET RESOUR 2021. [DOI: 10.1007/s12686-021-01196-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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15
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Fontes JT, Vieira PE, Ekrem T, Soares P, Costa FO. BAGS: An automated Barcode, Audit & Grade System for DNA barcode reference libraries. Mol Ecol Resour 2020; 21:573-583. [PMID: 33000878 DOI: 10.1111/1755-0998.13262] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 09/01/2020] [Accepted: 09/07/2020] [Indexed: 01/12/2023]
Abstract
Biodiversity studies greatly benefit from molecular tools, such as DNA metabarcoding, which provides an effective identification tool in biomonitoring and conservation programmes. The accuracy of species-level assignment, and consequent taxonomic coverage, relies on comprehensive DNA barcode reference libraries. The role of these libraries is to support species identification, but accidental errors in the generation of the barcodes may compromise their accuracy. Here, we present an R-based application, Barcode, Audit & Grade System (BAGS) (https://github.com/tadeu95/BAGS), that performs automated auditing and annotation of cytochrome c oxidase subunit I (COI) sequences libraries, for a given taxonomic group of animals, available in the Barcode of Life Data System (BOLD). This is followed by implementing a qualitative ranking system that assigns one of five grades (A to E) to each species in the reference library, according to the attributes of the data and congruency of species names with sequences clustered in barcode index numbers (BINs). Our goal is to allow researchers to obtain the most useful and reliable data, highlighting and segregating records according to their congruency. Different tests were performed to perceive its usefulness and limitations. BAGS fulfils a significant gap in the current landscape of DNA barcoding research tools by quickly screening reference libraries to gauge the congruence status of data and facilitate the triage of ambiguous data for posterior review. Thereby, BAGS has the potential to become a valuable addition in forthcoming DNA metabarcoding studies, in the long term contributing to globally improve the quality and reliability of the public reference libraries.
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Affiliation(s)
- João T Fontes
- Department of Biology, CBMA - Centre of Molecular and Environmental Biology, University of Minho, Braga, Portugal.,Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Minho, Portugal
| | - Pedro E Vieira
- Department of Biology, CBMA - Centre of Molecular and Environmental Biology, University of Minho, Braga, Portugal.,Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Minho, Portugal
| | - Torbjørn Ekrem
- Department of Natural History, NTNU University Museum, Trondheim, Norway
| | - Pedro Soares
- Department of Biology, CBMA - Centre of Molecular and Environmental Biology, University of Minho, Braga, Portugal.,Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Minho, Portugal
| | - Filipe O Costa
- Department of Biology, CBMA - Centre of Molecular and Environmental Biology, University of Minho, Braga, Portugal.,Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, Minho, Portugal
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16
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Raupach MJ, Hannig K, Morinière J, Hendrich L. A DNA barcode library for ground beetles of Germany: the genus Pterostichus Bonelli, 1810 and allied taxa (Insecta, Coleoptera, Carabidae). Zookeys 2020; 980:93-117. [PMID: 33192140 PMCID: PMC7642132 DOI: 10.3897/zookeys.980.55979] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 09/04/2020] [Indexed: 11/12/2022] Open
Abstract
Species of the ground beetle genus Pterostichus Bonelli, 1810 are some of the most common carabids in Europe. This publication provides a first comprehensive DNA barcode library for this genus and allied taxa including Abax Bonelli, 1810, Molops Bonelli, 1810, Poecilus Bonelli, 1810, and Stomis Clairville, 1806 for Germany and Central Europe in general. DNA barcodes were analyzed from 609 individuals that represent 51 species, including sequences from previous studies as well as more than 198 newly generated sequences. The results showed a 1:1 correspondence between BIN and traditionally recognized species for 44 species (86%), whereas two (4%) species were characterized by two BINs. Three BINs were found for one species (2%), while one BIN for two species was revealed for two species pairs (8%). Low interspecific distances with maximum pairwise K2P values below 2.2% were found for four species pairs. Haplotype sharing was found for two closely related species pairs: Pterostichusadstrictus Eschscholtz, 1823/Pterostichusoblongopunctatus (Fabricius, 1787) and Pterostichusnigrita Paykull, 1790/Pterostichusrhaeticus Heer, 1837. In contrast to this, high intraspecific sequence divergences with values above 2.2% were shown for three species (Molopspiceus (Panzer, 1793), Pterostichuspanzeri (Panzer, 1805), Pterostichusstrenuus (Panzer, 1793)). Summarizing the results, the present DNA barcode library does not only allow the identification of most of the analyzed species, but also provides valuable information for alpha-taxonomy as well as for ecological and evolutionary research. This library represents another step in building a comprehensive DNA barcode library of ground beetles as part of modern biodiversity research.
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Affiliation(s)
- Michael J Raupach
- Sektion Hemiptera, Bavarian State Collection of Zoology (SNSB - ZSM), Münchhausenstraße 21, 81247 München, Germany
| | | | - Jérome Morinière
- AIM - Advanced Identification Methods GmbH, Spinnereistraße 11, 04179 Leipzig
| | - Lars Hendrich
- Sektion Insecta varia, Bavarian State Collection of Zoology (SNSB - ZSM), Münchhausenstraße 21, 81247 München, Germany
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17
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Distant hybrids of Heliocidaris crassispina (♀) and Strongylocentrotus intermedius (♂): identification and mtDNA heteroplasmy analysis. BMC Evol Biol 2020; 20:101. [PMID: 32781979 PMCID: PMC7422570 DOI: 10.1186/s12862-020-01667-8] [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: 02/19/2020] [Accepted: 07/30/2020] [Indexed: 11/27/2022] Open
Abstract
Background Distant hybridization between the sea urchin Heliocidaris crassispina (♀) and the sea urchin Strongylocentrotus intermedius (♂) was successfully performed under laboratory conditions. A new variety of hybrid sea urchin (HS hybrid) was obtained. However, the early-development success rates for the HS hybrids were significantly lower than those of purebred H. crassispina or S. intermedius offspring. In addition, it was difficult to distinguish the HS-hybrid adults from the pure H. crassispina adults, which might lead to confusion in subsequent breeding attempts. In this study, we attempted to develop a method to quickly and effectively identify HS hybrids, and to preliminarily investigate the molecular mechanisms underlying the poor early-development success rates in the HS hybrids. Results The hybrid sea urchins (HS hybrids) were identified both morphologically and molecularly. There were no significant differences in the test height to test diameter ratios between the HS hybrids and the parents. The number and arrangement of ambulacral pore pairs in the HS hybrids differed from those of the parental lines, which might serve as a useful morphological character for the identification of the HS hybrids. A primer pair that identified the HS hybrids was screened by comparing the mitochondrial genomes of the parental lines. Moreover, paternal leakage induced mitochondrial DNA heteroplasmy in the HS hybrids, which might explain the low rates of early development success in these hybrids. Conclusions The distant-hybrid sea urchins were accurately identified using comparative morphological and molecular genetic methods. The first evidence of mtDNA heteroplasmy after the distant hybridization of an echinoderm was also provided.
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18
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Arruda PSS, Ferreira DC, Oliveira C, Venere PC. DNA Barcoding Reveals High Levels of Divergence among Mitochondrial Lineages of Brycon (Characiformes, Bryconidae). Genes (Basel) 2019; 10:genes10090639. [PMID: 31450860 PMCID: PMC6769914 DOI: 10.3390/genes10090639] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 08/20/2019] [Accepted: 08/21/2019] [Indexed: 02/02/2023] Open
Abstract
Brycon is an important group of Neotropical fish and the principal genus of the family Bryconidae, with 44 valid species that are found in some Central American rivers and practically all the major hydrographic basins of South America. These fish are medium to large in size, migratory, omnivorous, important seed dispersers for riparian forests, and bioindicators of environmental quality, given that they are found preferentially in rivers with clean, well oxygenated water. Many Brycon species are important fishery resources and some are farmed. Morphological and molecular studies have nevertheless indicated that the group is not monophyletic and has a number of unresolved taxonomic problems. Given this, the present study aimed to identify the Molecular Operational Taxonomic Units (MOTUs) of the genus using the mitochondrial cytochrome c oxidase I (COI) gene, with analyses of genetics distance (NJ), maximum likelihood (ML), and Bayesian Inference (BI), combined with two different species delimitation approaches (GMYC and ABGD). The results indicate that at least 31 MOTUs exist within the 18 species identified a priori based on their morphology. Many of these lineages require further investigation for a more definitive classification.
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Affiliation(s)
- Pábila S S Arruda
- Programa de Pós-Graduação em Ecologia e Conservação da Biodiversidade, Instituto de Biociências, Universidade Federal de Mato Grosso, Avenida Fernando Correia da Costa, 2367, Cuiabá, Mato Grosso 78060-900, Brazil
| | - Daniela C Ferreira
- Departamento de Biologia e Zoologia, Instituto de Biociências, Universidade Federal de Mato Grosso, Avenida Fernando Correia da Costa, 2367, Cuiabá, Mato Grosso 78060-900, Brazil
| | - Claudio Oliveira
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho - UNESP, Rubião Jr S-N, Botucatu, São Paulo 18618-970, Brazil
| | - Paulo C Venere
- Departamento de Biologia e Zoologia, Instituto de Biociências, Universidade Federal de Mato Grosso, Avenida Fernando Correia da Costa, 2367, Cuiabá, Mato Grosso 78060-900, Brazil.
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19
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Metabarcoding of marine environmental DNA based on mitochondrial and nuclear genes. Sci Rep 2018; 8:14822. [PMID: 30287908 PMCID: PMC6172225 DOI: 10.1038/s41598-018-32917-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 09/17/2018] [Indexed: 11/17/2022] Open
Abstract
We establish the new approach of environmental DNA (eDNA) analyses for the North Sea. Our study uses a multigene approach, including the mitochondrial cytochrome-c-oxidase subunit I (COI) gene for analyzing species composition and the nuclear hypervariable region V8 of 18S rDNA for analyzing supraspecific biodiversity. A new minibarcode primer (124 bp) was created on the basis of a metazoan COI barcode library with 506 species and tested in silico, in vitro, and in situ. We applied high throughput sequencing to filtrates of 23 near-bottom water samples taken at three seasons from 14 stations. The set of COI primers allowed amplification of mitochondrial minibarcodes for diverse metazoan phyla and the differentiation at the species level for more than 99% of the specimens in the dataset. Our results revealed that the number of sequences is not consistent with proportions in the given DNA mixture. Altogether, environmental sequences could be assigned to 114 species and to 12 metazoan phyla. A spatial distribution of taxa recovered by eDNA was congruent with known distributions. Finally, the successful detection of species and biodiversity depends on a comprehensive sequence reference database. Our study offers a powerful tool for future biodiversity research, including the detection of nonnative species.
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20
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Ferrari A, Tinti F, Bertucci Maresca V, Velonà A, Cannas R, Thasitis I, Costa FO, Follesa MC, Golani D, Hemida F, Helyar SJ, Mancusi C, Mulas A, Serena F, Sion L, Stagioni M, Cariani A. Natural history and molecular evolution of demersal Mediterranean sharks and skates inferred by comparative phylogeographic and demographic analyses. PeerJ 2018; 6:e5560. [PMID: 30245927 PMCID: PMC6149499 DOI: 10.7717/peerj.5560] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 08/09/2018] [Indexed: 11/22/2022] Open
Abstract
Background The unique and complex paleoclimatic and paleogeographic events which affected the Mediterranean Sea since late Miocene deeply influenced the distribution and evolution of marine organisms and shaped their genetic structure. Following the Messinian salinity crisis and the sea-level fluctuations during the Pleistocene, several Mediterranean marine species developed deep genetic differentiation, and some underwent rapid radiation. Here, we consider two of the most prioritized groups for conservation in the light of their evolutionary history: sharks and rays (elasmobranchs). This paper deals with a comparative multispecies analysis of phylogeographic structure and historical demography in two pairs of sympatric, phylogenetically- and ecologically-related elasmobranchs, two scyliorhinid catsharks (Galeus melastomus, Scyliorhinus canicula) and two rajid skates (Raja clavata, Raja miraletus). Sampling and experimental analyses were designed to primarily test if the Sicilian Channel can be considered as effective eco-physiological barrier for Mediterranean demersal sympatric elasmobranchs. Methods The phylogeography and the historical demography of target species were inferred by analysing the nucleotide variation of three mitochondrial DNA markers (i.e., partial sequence of COI, NADH2 and CR) obtained from a total of 248 individuals sampled in the Western and Eastern Mediterranean Sea as well as in the adjacent northeastern Atlantic Ocean. Phylogeographic analysis was performed by haplotype networking and testing spatial genetic differentiation of samples (i.e., analysis of molecular variance and of principal components). Demographic history of Mediterranean populations was reconstructed using mismatch distribution and Bayesian Skyline Plot analyses. Results No spatial genetic differentiation was identified in either catshark species, while phylogeographic structure of lineages was identified in both skates, with R. miraletus more structured than R. clavata. However, such structuring of skate lineages was not consistent with the separation between Western and Eastern Mediterranean. Sudden demographic expansions occurred synchronously during the upper Pleistocene (40,000–60,000 years ago) in both skates and G. melastomus, likely related to optimal environmental conditions. In contrast, S. canicula experienced a slow and constant increase in population size over the last 350,000 years. Discussion The comparative analysis of phylogeographic and historical demographic patterns for the Mediterranean populations of these elasmobranchs reveals that historical phylogeographic breaks have not had a large impact on their microevolution. We hypothesize that interactions between environmental and ecological/physiological traits may have been the driving force in the microevolution of these demersal elasmobranch species in the Mediterranean rather than oceanographic barriers.
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Affiliation(s)
- Alice Ferrari
- Department of Biological, Geological & Environmental Sciences (BiGeA), University of Bologna, Bologna, Italy
| | - Fausto Tinti
- Department of Biological, Geological & Environmental Sciences (BiGeA), University of Bologna, Bologna, Italy
| | - Victoria Bertucci Maresca
- Department of Biological, Geological & Environmental Sciences (BiGeA), University of Bologna, Bologna, Italy.,Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Alessandro Velonà
- Department of Biological, Geological & Environmental Sciences (BiGeA), University of Bologna, Bologna, Italy
| | - Rita Cannas
- Department of Life Sciences and Environment, University of Cagliari, Cagliari, Italy
| | - Ioannis Thasitis
- Department of Fisheries and Marine Research, Ministry of Agriculture, Natural Resources and Environment, Nicosia, Cyprus
| | - Filipe Oliveira Costa
- Centre of Molecular and Environmental Biology (CBMA), University of Minho, Braga, Portugal
| | | | - Daniel Golani
- Department of Evolution, Systematics and Ecology, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Farid Hemida
- Ecole Nationale Supérieure des Sciences de la Mer et de Aménagement du Littoral (ENSSMAL), Algiers, Algeria
| | - Sarah J Helyar
- School of Biological Sciences, Institute for Global Food Security, The Queen's University Belfast, Belfast, United Kingdom
| | - Cecilia Mancusi
- Regional Agency for Environmental Protection-Toscana (ARPAT), Livorno, Italy
| | - Antonello Mulas
- Department of Life Sciences and Environment, University of Cagliari, Cagliari, Italy
| | - Fabrizio Serena
- Institute Coastal Marine Environment, Italian National Research Council (CNR-IAMC), Mazara del Vallo, Italy
| | - Letizia Sion
- Department of Biology, University of Bari, Bari, Italy
| | - Marco Stagioni
- Department of Biological, Geological & Environmental Sciences (BiGeA), University of Bologna, Bologna, Italy
| | - Alessia Cariani
- Department of Biological, Geological & Environmental Sciences (BiGeA), University of Bologna, Bologna, Italy
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21
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Iyiola OA, Nneji LM, Mustapha MK, Nzeh CG, Oladipo SO, Nneji IC, Okeyoyin AO, Nwani CD, Ugwumba OA, Ugwumba AAA, Faturoti EO, Wang Y, Chen J, Wang W, Adeola AC. DNA barcoding of economically important freshwater fish species from north-central Nigeria uncovers cryptic diversity. Ecol Evol 2018; 8:6932-6951. [PMID: 30073057 PMCID: PMC6065348 DOI: 10.1002/ece3.4210] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 04/17/2018] [Accepted: 04/22/2018] [Indexed: 11/25/2022] Open
Abstract
This study examines the utility of morphology and DNA barcoding in species identification of freshwater fishes from north-central Nigeria. We compared molecular data (mitochondrial cytochrome c oxidase subunit I (COI) sequences) of 136 de novo samples from 53 morphologically identified species alongside others in GenBank and BOLD databases. Using DNA sequence similarity-based (≥97% cutoff) identification technique, 50 (94.30%) and 24 (45.30%) species were identified to species level using GenBank and BOLD databases, respectively. Furthermore, we identified cases of taxonomic problems in 26 (49.00%) morphologically identified species. There were also four (7.10%) cases of mismatch in DNA barcoding in which our query sequence in GenBank and BOLD showed a sequence match with different species names. Using DNA barcode reference data, we also identified four unknown fish samples collected from fishermen to species level. Our Neighbor-joining (NJ) tree analysis recovers several intraspecific species clusters with strong bootstrap support (≥95%). Analysis uncovers two well-supported lineages within Schilbe intermedius. The Bayesian phylogenetic analyses of Nigerian S. intermedius with others from GenBank recover four lineages. Evidence of genetic structuring is consistent with geographic regions of sub-Saharan Africa. Thus, cryptic lineage diversity may illustrate species' adaptive responses to local environmental conditions. Finally, our study underscores the importance of incorporating morphology and DNA barcoding in species identification. Although developing a complete DNA barcode reference library for Nigerian ichthyofauna will facilitate species identification and diversity studies, taxonomic revisions of DNA sequences submitted in databases alongside voucher specimens are necessary for a reliable taxonomic and diversity inventory.
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Affiliation(s)
- Oluyinka A. Iyiola
- Department of ZoologyFaculty of Life SciencesUniversity of IlorinIlorinKwara StateNigeria
| | - Lotanna M. Nneji
- Kunming Institute of ZoologyChinese Academy of SciencesKunmingChina
- Sino‐Africa Joint Research CenterChinese Academy of SciencesKunmingChina
- Kunming College of Life ScienceUniversity of Chinese Academy of SciencesKunmingChina
| | - Moshood K. Mustapha
- Department of ZoologyFaculty of Life SciencesUniversity of IlorinIlorinKwara StateNigeria
| | - Chioma G. Nzeh
- Department of ZoologyFaculty of Life SciencesUniversity of IlorinIlorinKwara StateNigeria
| | - Segun O. Oladipo
- Department of Biosciences and BiotechnologyKwara State UniversityMaleteKwara StateNigeria
| | | | - Agboola O. Okeyoyin
- Nigerian National Park Service HeadquartersFederal Capital TerritoryAbujaNigeria
| | - Christopher D. Nwani
- Department of Zoology and Environmental BiologyUniversity of NigeriaNsukkaNigeria
| | - Obih A. Ugwumba
- Department of ZoologyUniversity of IbadanIbadanOyo StateNigeria
| | | | - Emmanuel O. Faturoti
- Department of Aquaculture and Fisheries ManagementUniversity of IbadanIbadanOyo StateNigeria
| | - Yun‐yu Wang
- Kunming Institute of ZoologyChinese Academy of SciencesKunmingChina
| | | | - Wen‐Zhi Wang
- Kunming Institute of ZoologyChinese Academy of SciencesKunmingChina
- Sino‐Africa Joint Research CenterChinese Academy of SciencesKunmingChina
- Wild Forensic CenterKunmingChina
| | - Adeniyi C. Adeola
- Kunming Institute of ZoologyChinese Academy of SciencesKunmingChina
- Sino‐Africa Joint Research CenterChinese Academy of SciencesKunmingChina
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Raupach MJ, Hannig K, Moriniére J, Hendrich L. A DNA barcode library for ground beetles of Germany: the genus Amara Bonelli, 1810 (Insecta, Coleoptera, Carabidae). Zookeys 2018; 759:57-80. [PMID: 29853775 PMCID: PMC5968077 DOI: 10.3897/zookeys.759.24129] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 03/27/2018] [Indexed: 01/08/2023] Open
Abstract
The genus Amara Bonelli, 1810 is a very speciose and taxonomically difficult genus of the Carabidae. The identification of many of the species is accomplished with considerable difficulty, in particular for females and immature stages. In this study the effectiveness of DNA barcoding, the most popular method for molecular species identification, was examined to discriminate various species of this genus from Central Europe. DNA barcodes from 690 individuals and 47 species were analysed, including sequences from previous studies and more than 350 newly generated DNA barcodes. Our analysis revealed unique BINs for 38 species (81%). Interspecific K2P distances below 2.2% were found for three species pairs and one species trio, including haplotype sharing between Amara alpina/Amara torrida and Amara communis/Amara convexior/Amara makolskii. This study represents another step in generating an extensive reference library of DNA barcodes for carabids, highly valuable bioindicators for characterizing disturbances in various habitats.
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Affiliation(s)
- Michael J. Raupach
- Institute for Biology and Environmental Sciences, Carl von Ossietzky University Oldenburg, Carl von Ossietzky Straße 9-11, 26111 Oldenburg, Germany
| | | | - Jérôme Moriniére
- Taxonomic coordinator – German Barcode of Life (GBOL), Bavarian State Collection of Zoology (SNSB – ZSM), Münchhausenstraße 21, 81247 München, Germany
| | - Lars Hendrich
- Sektion Insecta varia, Bavarian State Collection of Zoology (SNSB – ZSM), Münchhausenstraße 21, 81247 München, Germany
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23
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Beermann J, Westbury MV, Hofreiter M, Hilgers L, Deister F, Neumann H, Raupach MJ. Cryptic species in a well-known habitat: applying taxonomics to the amphipod genus Epimeria (Crustacea, Peracarida). Sci Rep 2018; 8:6893. [PMID: 29720606 PMCID: PMC5931980 DOI: 10.1038/s41598-018-25225-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 04/17/2018] [Indexed: 11/19/2022] Open
Abstract
Taxonomy plays a central role in biological sciences. It provides a communication system for scientists as it aims to enable correct identification of the studied organisms. As a consequence, species descriptions should seek to include as much available information as possible at species level to follow an integrative concept of 'taxonomics'. Here, we describe the cryptic species Epimeria frankei sp. nov. from the North Sea, and also redescribe its sister species, Epimeria cornigera. The morphological information obtained is substantiated by DNA barcodes and complete nuclear 18S rRNA gene sequences. In addition, we provide, for the first time, full mitochondrial genome data as part of a metazoan species description for a holotype, as well as the neotype. This study represents the first successful implementation of the recently proposed concept of taxonomics, using data from high-throughput technologies for integrative taxonomic studies, allowing the highest level of confidence for both biodiversity and ecological research.
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Affiliation(s)
- Jan Beermann
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Department of Functional Ecology, PO Box 120161, 27515, Bremerhaven, Germany.
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Biologische Anstalt Helgoland, Helgoland, Germany.
- Helmholtz Institute for Functional Marine Biodiversity, Oldenburg, Germany.
| | - Michael V Westbury
- University of Potsdam, Institute for Biochemistry and Biology, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany
| | - Michael Hofreiter
- University of Potsdam, Institute for Biochemistry and Biology, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany
| | - Leon Hilgers
- University of Potsdam, Institute for Biochemistry and Biology, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstr. 43, 10115, Berlin, Germany
| | - Fabian Deister
- Carl von Ossietzky University Oldenburg, Institute for Biology and Environmental Sciences, PO Box 2503, 26111, Oldenburg, Germany
| | - Hermann Neumann
- Senckenberg am Meer, Department for Marine Research, Südstrand 40, 26382, Wilhelmshaven, Germany
| | - Michael J Raupach
- Carl von Ossietzky University Oldenburg, Institute for Biology and Environmental Sciences, PO Box 2503, 26111, Oldenburg, Germany
- Senckenberg am Meer, German Center of Marine Biodiversity (DZMB), Südstrand 44, 26382, Wilhelmshaven, Germany
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Recognition and Distribution of Two North Atlantic Gadiculus Species, G. argenteus and G. thori (Gadidae), Based on Otolith Morphology, Larval Pigmentation, Molecular Evidence, Morphometrics and Meristics. FISHES 2017. [DOI: 10.3390/fishes2030015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Koroiva R, Pepinelli M, Rodrigues ME, Roque FDO, Lorenz-Lemke AP, Kvist S. DNA barcoding of odonates from the Upper Plata basin: Database creation and genetic diversity estimation. PLoS One 2017; 12:e0182283. [PMID: 28763495 PMCID: PMC5538745 DOI: 10.1371/journal.pone.0182283] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 07/14/2017] [Indexed: 11/18/2022] Open
Abstract
We present a DNA barcoding study of Neotropical odonates from the Upper Plata basin, Brazil. A total of 38 species were collected in a transition region of "Cerrado" and Atlantic Forest, both regarded as biological hotspots, and 130 cytochrome c oxidase subunit I (COI) barcodes were generated for the collected specimens. The distinct gap between intraspecific (0-2%) and interspecific variation (15% and above) in COI, and resulting separation of Barcode Index Numbers (BIN), allowed for successful identification of specimens in 94% of cases. The 6% fail rate was due to a shared BIN between two separate nominal species. DNA barcoding, based on COI, thus seems to be a reliable and efficient tool for identifying Neotropical odonate specimens down to the species level. These results underscore the utility of DNA barcoding to aid specimen identification in diverse biological hotspots, areas that require urgent action regarding taxonomic surveys and biodiversity conservation.
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Affiliation(s)
- Ricardo Koroiva
- Ecology and Conservation Graduate Program, Universidade Federal de Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
- Laboratório de Ecologia, Universidade Federal de Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
| | - Mateus Pepinelli
- Department of Natural History, Royal Ontario Museum, Toronto, Ontario, Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Marciel Elio Rodrigues
- Laboratório de Organismos Aquáticos, Universidade Estadual de Santa Cruz, Ilhéus, Bahia, Brazil
| | - Fabio de Oliveira Roque
- Laboratório de Ecologia, Universidade Federal de Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
| | - Aline Pedroso Lorenz-Lemke
- Laboratório de Evolução e Biodiversidade, Universidade Federal de Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
| | - Sebastian Kvist
- Department of Natural History, Royal Ontario Museum, Toronto, Ontario, Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
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Zahiri R, Lafontaine JD, Schmidt BC, deWaard JR, Zakharov EV, Hebert PDN. Probing planetary biodiversity with DNA barcodes: The Noctuoidea of North America. PLoS One 2017; 12:e0178548. [PMID: 28570635 PMCID: PMC5453547 DOI: 10.1371/journal.pone.0178548] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 05/15/2017] [Indexed: 11/18/2022] Open
Abstract
This study reports the assembly of a DNA barcode reference library for species in the lepidopteran superfamily Noctuoidea from Canada and the USA. Based on the analysis of 69,378 specimens, the library provides coverage for 97.3% of the noctuoid fauna (3565 of 3664 species). In addition to verifying the strong performance of DNA barcodes in the discrimination of these species, the results indicate close congruence between the number of species analyzed (3565) and the number of sequence clusters (3816) recognized by the Barcode Index Number (BIN) system. Distributional patterns across 12 North American ecoregions are examined for the 3251 species that have GPS data while BIN analysis is used to quantify overlap between the noctuoid faunas of North America and other zoogeographic regions. This analysis reveals that 90% of North American noctuoids are endemic and that just 7.5% and 1.8% of BINs are shared with the Neotropics and with the Palearctic, respectively. One third (29) of the latter species are recent introductions and, as expected, they possess low intraspecific divergences.
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Affiliation(s)
- Reza Zahiri
- Canadian Food Inspection Agency, Ottawa Plant Laboratory, Entomology Unit, Ottawa, Ontario, Canada
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - J. Donald Lafontaine
- Agriculture and Agri-Food Canada, Biodiversity Program, Canadian National Collection of Insects, Arachnids, and Nematodes, Ottawa, Ontario, Canada
| | - B. Christian Schmidt
- Agriculture and Agri-Food Canada, Biodiversity Program, Canadian National Collection of Insects, Arachnids, and Nematodes, Ottawa, Ontario, Canada
| | - Jeremy R. deWaard
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Evgeny V. Zakharov
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Paul D. N. Hebert
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
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More RP, Mane RC, Purohit HJ. matK-QR classifier: a patterns based approach for plant species identification. BioData Min 2016; 9:39. [PMID: 27990177 PMCID: PMC5148893 DOI: 10.1186/s13040-016-0120-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 12/02/2016] [Indexed: 12/24/2022] Open
Abstract
Background DNA barcoding is widely used and most efficient approach that facilitates rapid and accurate identification of plant species based on the short standardized segment of the genome. The nucleotide sequences of maturaseK (matK) and ribulose-1, 5-bisphosphate carboxylase (rbcL) marker loci are commonly used in plant species identification. Here, we present a new and highly efficient approach for identifying a unique set of discriminating nucleotide patterns to generate a signature (i.e. regular expression) for plant species identification. Methods In order to generate molecular signatures, we used matK and rbcL loci datasets, which encompass 125 plant species in 52 genera reported by the CBOL plant working group. Initially, we performed Multiple Sequence Alignment (MSA) of all species followed by Position Specific Scoring Matrix (PSSM) for both loci to achieve a percentage of discrimination among species. Further, we detected Discriminating Patterns (DP) at genus and species level using PSSM for the matK dataset. Combining DP and consecutive pattern distances, we generated molecular signatures for each species. Finally, we performed a comparative assessment of these signatures with the existing methods including BLASTn, Support Vector Machines (SVM), Jrip-RIPPER, J48 (C4.5 algorithm), and the Naïve Bayes (NB) methods against NCBI-GenBank matK dataset. Results Due to the higher discrimination success obtained with the matK as compared to the rbcL, we selected matK gene for signature generation. We generated signatures for 60 species based on identified discriminating patterns at genus and species level. Our comparative assessment results suggest that a total of 46 out of 60 species could be correctly identified using generated signatures, followed by BLASTn (34 species), SVM (18 species), C4.5 (7 species), NB (4 species) and RIPPER (3 species) methods As a final outcome of this study, we converted signatures into QR codes and developed a software matK-QR Classifier (http://www.neeri.res.in/matk_classifier/index.htm), which search signatures in the query matK gene sequences and predict corresponding plant species. Conclusions This novel approach of employing pattern-based signatures opens new avenues for the classification of species. In addition to existing methods, we believe that matK-QR Classifier would be a valuable tool for molecular taxonomists enabling precise identification of plant species. Electronic supplementary material The online version of this article (doi:10.1186/s13040-016-0120-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ravi Prabhakar More
- Environmental Genomics Division, CSIR-National Environmental Engineering Research Institute, Nagpur, 440020 Maharashtra India ; Present Institute: Division of Molecular Entomology, ICAR- National Bureau of Agricultural Insect Resources (NBAIR), Hebbal, Bengaluru, 560024 Karnataka India
| | | | - Hemant J Purohit
- Environmental Genomics Division, CSIR-National Environmental Engineering Research Institute, Nagpur, 440020 Maharashtra India
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28
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Geiger MF, Moriniere J, Hausmann A, Haszprunar G, Wägele W, Hebert PDN, Rulik B. Testing the Global Malaise Trap Program - How well does the current barcode reference library identify flying insects in Germany? Biodivers Data J 2016:e10671. [PMID: 27932930 PMCID: PMC5136679 DOI: 10.3897/bdj.4.e10671] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 11/29/2016] [Indexed: 11/25/2022] Open
Abstract
Background Biodiversity patterns are inherently complex and difficult to comprehensively assess. Yet, deciphering shifts in species composition through time and space are crucial for efficient and successful management of ecosystem services, as well as for predicting change. To better understand species diversity patterns, Germany participated in the Global Malaise Trap Program, a world-wide collection program for arthropods using this sampling method followed by their DNA barcode analysis. Traps were deployed at two localities: “Nationalpark Bayerischer Wald” in Bavaria, the largest terrestrial Natura 2000 area in Germany, and the nature conservation area Landskrone, an EU habitats directive site in the Rhine Valley. Arthropods were collected from May to September to track shifts in the taxonomic composition and temporal succession at these locations. New information In total, 37,274 specimens were sorted and DNA barcoded, resulting in 5,301 different genetic clusters (BINs, Barcode Index Numbers, proxy for species) with just 7.6% of their BINs shared. Accumulation curves for the BIN count versus the number of specimens analyzed suggest that about 63% of the potential diversity at these sites was recovered with this single season of sampling. Diversity at both sites rose from May (496 & 565 BINs) to July (1,236 & 1,522 BINs) before decreasing in September (572 & 504 BINs). Unambiguous species names were assigned to 35% of the BINs (1,868) which represented 12,640 specimens. Another 7% of the BINs (386) with 1,988 specimens were assigned to genus, while 26% (1,390) with 12,092 specimens were only placed to a family. These results illustrate how a comprehensive DNA barcode reference library can identify unknown specimens, but also reveal how this potential is constrained by gaps in the quantity and quality of records in BOLD, especially for Hymenoptera and Diptera. As voucher specimens are available for morphological study, we invite taxonomic experts to assist in the identification of unnamed BINs.
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Affiliation(s)
| | | | | | | | - Wolfgang Wägele
- Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | - Paul D N Hebert
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Canada
| | - Björn Rulik
- Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
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Oliveira LM, Knebelsberger T, Landi M, Soares P, Raupach MJ, Costa FO. Assembling and auditing a comprehensive DNA barcode reference library for European marine fishes. JOURNAL OF FISH BIOLOGY 2016; 89:2741-2754. [PMID: 27739061 DOI: 10.1111/jfb.13169] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 09/06/2016] [Indexed: 06/06/2023]
Abstract
A large-scale comprehensive reference library of DNA barcodes for European marine fishes was assembled, allowing the evaluation of taxonomic uncertainties and species genetic diversity that were otherwise hidden in geographically restricted studies. A total of 4118 DNA barcodes were assigned to 358 species generating 366 Barcode Index Numbers (BIN). Initial examination revealed as much as 141 BIN discordances (more than one species in each BIN). After implementing an auditing and five-grade (A-E) annotation protocol, the number of discordant species BINs was reduced to 44 (13% grade E), while concordant species BINs amounted to 271 (78% grades A and B) and 14 other had insufficient data (grade D). Fifteen species displayed comparatively high intraspecific divergences ranging from 2·6 to 18·5% (grade C), which is biologically paramount information to be considered in fish species monitoring and stock assessment. On balance, this compilation contributed to the detection of 59 European fish species probably in need of taxonomic clarification or re-evaluation. The generalized implementation of an auditing and annotation protocol for reference libraries of DNA barcodes is recommended.
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Affiliation(s)
- L M Oliveira
- Center of Molecular and Environmental Biology (CBMA), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - T Knebelsberger
- Senckenberg am Meer, German Center for Marine Biodiversity Research (DZMB), Suedstrand 44, 26382, Wilhelmshaven, Germany
| | - M Landi
- Center of Molecular and Environmental Biology (CBMA), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - P Soares
- Center of Molecular and Environmental Biology (CBMA), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - M J Raupach
- Senckenberg am Meer, German Center for Marine Biodiversity Research (DZMB), Suedstrand 44, 26382, Wilhelmshaven, Germany
| | - F O Costa
- Center of Molecular and Environmental Biology (CBMA), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
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Thiel R, Knebelsberger T. How reliably can northeast Atlantic sand lances of the genera Ammodytes and Hyperoplus be distinguished? A comparative application of morphological and molecular methods. Zookeys 2016:139-64. [PMID: 27667958 PMCID: PMC5027774 DOI: 10.3897/zookeys.617.8866] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 08/06/2016] [Indexed: 11/21/2022] Open
Abstract
Accurate stock assessments for each of the dominant species of sand lances in the northeast Atlantic Ocean and adjacent areas are not available due to the lack of a reliable identification procedure; therefore, appropriate measures of fisheries management or conservation of sand lances cannot be implemented. In this study, detailed morphological and molecular features are assessed to discriminate between four species of sand lances belonging to the genera Ammodytes and Hyperoplus. Morphological characters described by earlier authors as useful for identification of the genera are confirmed, and two additional distinguishing characters are added. A combination of the following morphological characters is recommended to distinguish between the genera Hyperoplus and Ammodytes: the protrusibility of the premaxillae, the presence of hooked ends of the prevomer, the number of dermal plicae, and the pectoral-fin length as a percentage of the standard length. The discriminant function analysis revealed that morphometric data are not very useful to distinguish the species of each of the two genera. The following meristic characters improve the separation of Hyperopluslanceolatus from Hyperoplusimmaculatus: the number of lower arch gill rakers, total number of gill rakers, numbers of caudal vertebrae and total vertebrae, and numbers of dorsal-fin and anal-fin rays. It is confirmed that Ammodytestobianus differs from Ammodytesmarinus by its belly scales that are organised in tight chevrons, scales which are present over the musculature at the base of the caudal fin, as well as by the lower numbers of dermal plicae, dorsal-fin rays, and total vertebrae. In contrast to the morphological data, mitochondrial COI sequences (DNA barcodes) failed to separate unambiguously the four investigated species. Ammodytestobianus and Hyperopluslanceolatus showed an overlap between intraspecific and interspecific K2P genetic distances and cannot be reliably distinguished using the common DNA barcoding approach. Ammodytesmarinus and Hyperoplusimmaculatus exhibited gaps between intraspecific and interspecific K2P distances of 2.73 and 3.34% respectively, indicating that their DNA barcodes can be used for species identification. As an alternative, short nuclear Rhodopsin sequences were analysed and one diagnostic character was found for each of the species Ammodytesmarinus, Hyperopluslanceolatus, and Hyperoplusimmaculatus. Ammodytestobianus can be characterised by the lack of species-specific mutations when compared to the other three species. In contrast to COI, the short nuclear sequences represent a useful alternative for rapid species identification whenever an examination of morphological characters is not available.
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Affiliation(s)
- Ralf Thiel
- University of Hamburg, Center of Natural History, Zoological Museum, 20146 Hamburg, Germany
| | - Thomas Knebelsberger
- Senckenberg am Meer, German Centre for Marine Biodiversity Research (DZMB), 26382 Wilhelmshaven, Germany
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31
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Raupach MJ, Hannig K, Morinière J, Hendrich L. A DNA barcode library for ground beetles (Insecta, Coleoptera, Carabidae) of Germany: The genus Bembidion Latreille, 1802 and allied taxa. Zookeys 2016; 592:121-41. [PMID: 27408547 PMCID: PMC4926639 DOI: 10.3897/zookeys.592.8316] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 04/23/2016] [Indexed: 12/23/2022] Open
Abstract
As molecular identification method, DNA barcoding based on partial cytochrome c oxidase subunit 1 (COI) sequences has been proven to be a useful tool for species determination in many insect taxa including ground beetles. In this study we tested the effectiveness of DNA barcodes to discriminate species of the ground beetle genus Bembidion and some closely related taxa of Germany. DNA barcodes were obtained from 819 individuals and 78 species, including sequences from previous studies as well as more than 300 new generated DNA barcodes. We found a 1:1 correspondence between BIN and traditionally recognized species for 69 species (89%). Low interspecific distances with maximum pairwise K2P values below 2.2% were found for three species pairs, including two species pairs with haplotype sharing (Bembidion atrocaeruleum/Bembidion varicolor and Bembidion guttula/Bembidion mannerheimii). In contrast to this, deep intraspecific sequence divergences with distinct lineages were revealed for two species (Bembidion geniculatum/Ocys harpaloides). Our study emphasizes the use of DNA barcodes for the identification of the analyzed ground beetles species and represents an important step in building-up a comprehensive barcode library for the Carabidae in Germany and Central Europe as well.
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Affiliation(s)
- Michael J. Raupach
- Molecular Taxonomy of Marine Organisms, German Centre of Marine Biodiversity Research (DZMB), Senckenberg am Meer, Südstrand 44, 26382 Wilhelmshaven, Germany
| | | | - Jérome Morinière
- Taxonomic coordinator – Barcoding Fauna Bavarica, Bavarian State Collection of Zoology (SNSB – ZSM), Münchhausenstraße 21, 81247 München, Germany
| | - Lars Hendrich
- Sektion Insecta varia, Bavarian State Collection of Zoology (SNSB – ZSM), Münchhausenstraße 21, 81247 München, Germany
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Shen Y, Guan L, Wang D, Gan X. DNA barcoding and evaluation of genetic diversity in Cyprinidae fish in the midstream of the Yangtze River. Ecol Evol 2016; 6:2702-13. [PMID: 27066250 PMCID: PMC4798831 DOI: 10.1002/ece3.2060] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 01/31/2016] [Accepted: 02/02/2016] [Indexed: 11/29/2022] Open
Abstract
The Yangtze River is the longest river in China and is divided into upstream and mid-downstream regions by the Three Gorges (the natural barriers of the Yangtze River), resulting in a complex distribution of fish. Dramatic changes to habitat environments may ultimately threaten fish survival; thus, it is necessary to evaluate the genetic diversity and propose protective measures. Species identification is the most significant task in many fields of biological research and in conservation efforts. DNA barcoding, which constitutes the analysis of a short fragment of the mitochondrial cytochrome c oxidase subunit I (COI) sequence, has been widely used for species identification. In this study, we collected 561 COI barcode sequences from 35 fish from the midstream of the Yangtze River. The intraspecific distances of all species were below 2% (with the exception of Acheilognathus macropterus and Hemibarbus maculatus). Nevertheless, all species could be unambiguously identified from the trees, barcoding gaps and taxonomic resolution ratio values. Furthermore, the COI barcode diversity was found to be low (≤0.5%), with the exception of H. maculatus (0.87%), A. macropterus (2.02%) and Saurogobio dabryi (0.82%). No or few shared haplotypes were detected between the upstream and downstream populations for ten species with overall nucleotide diversities greater than 0.00%, which indicated the likelihood of significant population genetic structuring. Our analyses indicated that DNA barcoding is an effective tool for the identification of cyprinidae fish in the midstream of the Yangtze River. It is vital that some protective measures be taken immediately because of the low COI barcode diversity.
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Affiliation(s)
- Yanjun Shen
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of SciencesInstitute of HydrobiologyChinese Academy of SciencesWuhan430072HubeiChina
- University of Chinese Academy of SciencesBeijing100039China
| | - Lihong Guan
- College of Life Science and TechnologyXinxiang Medical UniversityHe'nan Xinxiang453003China
| | - Dengqiang Wang
- The Key Laboratory of Freshwater Biodiversity ConservationMinistry of AgricultureYangtze River Fisheries Research InstituteChinese Academy of Fishery SciencesWuhanChina
| | - Xiaoni Gan
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of SciencesInstitute of HydrobiologyChinese Academy of SciencesWuhan430072HubeiChina
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Raupach MJ, Radulovici AE. Looking back on a decade of barcoding crustaceans. Zookeys 2015; 539:53-81. [PMID: 26798245 PMCID: PMC4714055 DOI: 10.3897/zookeys.539.6530] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 10/20/2015] [Indexed: 02/07/2023] Open
Abstract
Species identification represents a pivotal component for large-scale biodiversity studies and conservation planning but represents a challenge for many taxa when using morphological traits only. Consequently, alternative identification methods based on molecular markers have been proposed. In this context, DNA barcoding has become a popular and accepted method for the identification of unknown animals across all life stages by comparison to a reference library. In this review we examine the progress of barcoding studies for the Crustacea using the Web of Science data base from 2003 to 2014. All references were classified in terms of taxonomy covered, subject area (identification/library, genetic variability, species descriptions, phylogenetics, methods, pseudogenes/numts), habitat, geographical area, authors, journals, citations, and the use of the Barcode of Life Data Systems (BOLD). Our analysis revealed a total number of 164 barcoding studies for crustaceans with a preference for malacostracan crustaceans, in particular Decapoda, and for building reference libraries in order to identify organisms. So far, BOLD did not establish itself as a popular informatics platform among carcinologists although it offers many advantages for standardized data storage, analyses and publication.
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Affiliation(s)
- Michael J. Raupach
- Molecular Taxonomy of Marine Organisms, German Centre of Marine Biodiversity Research (DZMB), Senckenberg am Meer, Südstrand 44, 26382 Wilhelmshaven, Germany
| | - Adriana E. Radulovici
- Biodiversity Institute of Ontario (BIO), University of Guelph, 50 Stone Road E, Guelph (ON) N1G 2W1, Ontario, Canada
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Landi M, Dimech M, Arculeo M, Biondo G, Martins R, Carneiro M, Carvalho GR, Brutto SL, Costa FO. DNA barcoding for species assignment: the case of Mediterranean marine fishes. PLoS One 2014; 9:e106135. [PMID: 25222272 PMCID: PMC4164363 DOI: 10.1371/journal.pone.0106135] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Accepted: 08/01/2014] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND DNA barcoding enhances the prospects for species-level identifications globally using a standardized and authenticated DNA-based approach. Reference libraries comprising validated DNA barcodes (COI) constitute robust datasets for testing query sequences, providing considerable utility to identify marine fish and other organisms. Here we test the feasibility of using DNA barcoding to assign species to tissue samples from fish collected in the central Mediterranean Sea, a major contributor to the European marine ichthyofaunal diversity. METHODOLOGY/PRINCIPAL FINDINGS A dataset of 1278 DNA barcodes, representing 218 marine fish species, was used to test the utility of DNA barcodes to assign species from query sequences. We tested query sequences against 1) a reference library of ranked DNA barcodes from the neighbouring North East Atlantic, and 2) the public databases BOLD and GenBank. In the first case, a reference library comprising DNA barcodes with reliability grades for 146 fish species was used as diagnostic dataset to screen 486 query DNA sequences from fish specimens collected in the central basin of the Mediterranean Sea. Of all query sequences suitable for comparisons 98% were unambiguously confirmed through complete match with reference DNA barcodes. In the second case, it was possible to assign species to 83% (BOLD-IDS) and 72% (GenBank) of the sequences from the Mediterranean. Relatively high intraspecific genetic distances were found in 7 species (2.2%-18.74%), most of them of high commercial relevance, suggesting possible cryptic species. CONCLUSION/SIGNIFICANCE We emphasize the discriminatory power of COI barcodes and their application to cases requiring species level resolution starting from query sequences. Results highlight the value of public reference libraries of reliability grade-annotated DNA barcodes, to identify species from different geographical origins. The ability to assign species with high precision from DNA samples of disparate quality and origin has major utility in several fields, from fisheries and conservation programs to control of fish products authenticity.
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Affiliation(s)
- Monica Landi
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Braga, Portugal
| | - Mark Dimech
- Malta Centre for Fisheries Science (MCFS), Fort San Lucjan Marsaxlokk, Malta
| | - Marco Arculeo
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), University of Palermo, Palermo, Italy
| | - Girolama Biondo
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), University of Palermo, Palermo, Italy
| | - Rogelia Martins
- Modelling and Management Fishery Resources Division (DIV-RP), Instituto Português do Mar e da Atmosfera, Lisboa, Portugal
| | - Miguel Carneiro
- Modelling and Management Fishery Resources Division (DIV-RP), Instituto Português do Mar e da Atmosfera, Lisboa, Portugal
| | - Gary Robert Carvalho
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Bangor, United Kingdom
| | - Sabrina Lo Brutto
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), University of Palermo, Palermo, Italy
| | - Filipe O. Costa
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Braga, Portugal
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