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Panthum T, Ariyaphong N, Wattanadilokchatkun P, Singchat W, Ahmad SF, Kraichak E, Dokkaew S, Muangmai N, Han K, Duengkae P, Srikulnath K. Quality control of fighting fish nucleotide sequences in public repositories reveals a dark matter of systematic taxonomic implication. Genes Genomics 2023; 45:169-181. [PMID: 36512198 DOI: 10.1007/s13258-022-01353-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 12/02/2022] [Indexed: 12/15/2022]
Abstract
BACKGROUND The number of nucleotide sequences in public repositories has exploded recently. However, the data contain errors, leading to incorrect species identification. Several fighting fish (Betta spp.) are poorly described, with unresolved cryptic species complexes masking undescribed species. Here, DNA barcoding was used to detect erroneous sequences in public repositories. OBJECTIVE This study reflects the current quantitative and qualitative status of DNA barcoding in fighting fish and provides a rapid and reliable identification tool. METHODS A total of 1034 barcode sequences were analyzed from mitochondrial cytochrome c oxidase I (COI) and cytochrome b (Cytb) genes from 71 fighting fish species. RESULTS The nearest neighbor test showed the highest percentage of intraspecific nearest neighbors at 93.41% for COI and 91.67% for Cytb, which can be used as reference barcodes for certain taxa. Intraspecific variation was usually less than 13%, while most species differed by more than 54%. The barcoding gap, calculated from the difference between inter- and intraspecific sequence divergences, was negative in the COI data set indicating overlapping intra- and interspecific sequence divergence. Sequence saturation was observed in the Cytb data set but not in the COI data set. CONCLUSION The COI gene should thus be used as the main barcoding marker for fighting fish.
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Affiliation(s)
- Thitipong Panthum
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Faculty of Science, Interdisciplinary Graduate Program in Bioscience, Kasetsart University, Bangkok, 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Nattakan Ariyaphong
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Pish Wattanadilokchatkun
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Master of Science Program in Fishery Science and Technology (International Program), Faculty of Fisheries, Kasetsart University, Bangkok, 10900, Thailand
| | - Worapong Singchat
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Syed Farhan Ahmad
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Ekaphan Kraichak
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Department of Botany, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Sahabhop Dokkaew
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Department of Aquaculture, Faculty of Fisheries, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Narongrit Muangmai
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Department of Fishery Biology, Faculty of Fisheries, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Kyudong Han
- Department of Microbiology, Dankook University, Cheonan, 31116, Korea
- Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan, 31116, Korea
| | - Prateep Duengkae
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Kornsorn Srikulnath
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.
- Faculty of Science, Interdisciplinary Graduate Program in Bioscience, Kasetsart University, Bangkok, 10900, Thailand.
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.
- Master of Science Program in Fishery Science and Technology (International Program), Faculty of Fisheries, Kasetsart University, Bangkok, 10900, Thailand.
- Amphibian Research Center, Hiroshima University, 1-3-1, Kagamiyama, Higashihiroshima, 739-8526, Japan.
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Ruiz-García M, Pinedo-Castro M, Shostell JM. Comparative phylogeography among eight Neotropical wild cat species: no single evolutionary pattern. Biol J Linn Soc Lond 2022. [DOI: 10.1093/biolinnean/blab170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
The felid species of South America are thought to have arrived on the continent during the Great American Biotic Interchange (GABI) in the Pleistocene. However, molecular and palaeontological data do not agree on how this event affected speciation in felids. Here, we determine both the number of colonization events and the period when felines first migrated from North America to South America. In addition, we evaluate whether similar evolutionary events could have affected the eight Neotropical cat species in their levels of genetic diversity, spatial genetic structure and demographic changes. We analysed four concatenated mitochondrial genes of the jaguar, ocelot, margay, tigrina, pampas cat, Andean cat, puma and jaguarundi. The samples were representative of a wide distribution of these species in Central and South America. Our analysis suggests either three or four colonization events from North America to South America over the past 3 Myr, followed by subsequent speciation events and the attainment of high or very high genetic diversity levels for seven of the species. No unique evolutionary process was detected for any of the current Neotropical cat species.
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Affiliation(s)
- Manuel Ruiz-García
- Laboratorio de Genética de Poblaciones Molecular-Biología Evolutiva, Departamento de Biología, Facultad de Ciencias, Pontificia Universidad Javeriana, Cra 7A, No. 43-82, Bogotá DC, Colombia
| | - Myreya Pinedo-Castro
- Laboratorio de Genética de Poblaciones Molecular-Biología Evolutiva, Departamento de Biología, Facultad de Ciencias, Pontificia Universidad Javeriana, Cra 7A, No. 43-82, Bogotá DC, Colombia
| | - Joseph Mark Shostell
- Math, Science and Technology Department, University of Minnesota Crookston, 2900 University Avenue, Crookston, MN 56716, USA
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3
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Geographically well-distributed citizen science data reveals range-wide variation in the chipping sparrow's simple song. Anim Behav 2020. [DOI: 10.1016/j.anbehav.2019.12.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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4
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Avigliano E, Rosso JJ, Lijtmaer D, Ondarza P, Piacentini L, Izquierdo M, Cirigliano A, Romano G, Nuñez Bustos E, Porta A, Mabragaña E, Grassi E, Palermo J, Bukowski B, Tubaro P, Schenone N. Biodiversity and threats in non-protected areas: A multidisciplinary and multi-taxa approach focused on the Atlantic Forest. Heliyon 2019; 5:e02292. [PMID: 31497670 PMCID: PMC6722266 DOI: 10.1016/j.heliyon.2019.e02292] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 07/04/2019] [Accepted: 08/08/2019] [Indexed: 01/15/2023] Open
Abstract
Along many decades, protected environments were targeted by the scientific community for ecological research and for the collection of scientific information related to environmental aspects and biodiversity. However, most of the territory in hotspot regions with weak or even non legal protection has been left aside. These non-protected areas (NPA) could host high biodiversity values. This paper addresses how scientific effort on a NPA (CIAR) of 700 ha from the Atlantic Rain Forest, generates new information and tools for large-scale environmental and biodiversity management in NPAs. Information published during the last decade was summarized and complemented with subsequent novel data about biodiversity (new species, first records, DNA and chemical analyses, etc.). The results showed: 1 new genus (arachnid), 6 new species and several putative new species (fish and arthropod), 6 vulnerable species (bird and mammal) and 36 first records for Argentina (fish, arthropod, platyhelminth and fungi). When compared with protected natural areas of the same biome, the CIAR showed highly valuable aspects for fauna and environment conservation, positioning this NPA as a worldwide hotspot for some taxa. Indeed, when compared to international hotspots in a coordinated Malaise trap program, the CIAR showed 8,651 different barcode index numbers (∼species) of arthropods, 80% of which had not been previously barcoded. Molecules like Inoscavin A, with antifungal activity against phytopathogens, was isolated for the first time in Phellinus merrillii fungi. The study of major threats derived from anthropic activities measured 20 trace elements, 18 pesticides (i.e. endosulfans, chlorpyrifos, DDTs, HCHs) and 27 pharmaceuticals and drugs (i.e. benzoylecgonine and norfluoxetine) in different biotic and abiotic matrices (water, sediment, fish and air biomonitors). This integrated data analysis shows that biodiversity research in NPA is being undervalued and how multidisciplinary and multi-taxa surveys creates a new arena for research and a pathway towards sustainable development in emerging countries with biodiversity hotspots.
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Affiliation(s)
- Esteban Avigliano
- Centro de Investigaciones Antonia Ramos (CIAR), Fundación Bosques Nativos Argentinos, Camino Balneario s/n, Villa Bonita, Misiones, Argentina
- Instituto de Investigaciones en Producción Animal (INPA-CONICET-UBA), Universidad de Buenos Aires, Av. Chorroarín 280, (C1427CWO), Buenos Aires, Argentina
| | - Juan Jose Rosso
- Grupo de Biotaxonomía Morfológica y Molecular de Peces (BIMOPE), Instituto de Investigaciones Marinas y Costeras, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata (CONICET), Dean Funes 3350, (B7600), Mar del Plata, Argentina
| | - Dario Lijtmaer
- Museo Argentino de Ciencias Naturales “Bernardino Rivadavia” (MACN-CONICET), Av. Angel Gallardo 470, (C1405DJR), Buenos Aires, Argentina
| | - Paola Ondarza
- Laboratorio de Ecotoxicología y Contaminación Ambiental, Instituto de Investigaciones Marinas y Costeras, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata (CONICET), Dean Funes 3350, (B7600), Mar del Plata, Argentina
| | - Luis Piacentini
- Museo Argentino de Ciencias Naturales “Bernardino Rivadavia” (MACN-CONICET), Av. Angel Gallardo 470, (C1405DJR), Buenos Aires, Argentina
| | - Matías Izquierdo
- Laboratorio de Biología Reproductiva y Evolución, Instituto de Diversidad y Ecología Animal (IDEA-UNC-CONICET), Facultad de Ciencias Exactas Físicas y Naturales, Universidad Nacional de Córdoba. Av. Velez Sarsfield 299 (X5000 JJC), Córdoba, Argentina
| | - Adriana Cirigliano
- Departamento de Química Orgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, (1428), Buenos Aires, Argentina
| | - Gonzalo Romano
- Departamento de Biología, Facultad de Ciencias Naturales, Universidad Nacional de la Patagonia San Juan Bosco (CONICET), Ruta 259 km 16.4, (9000), Esquel, Chubut, Argentina
| | - Ezequiel Nuñez Bustos
- Museo Argentino de Ciencias Naturales “Bernardino Rivadavia” (MACN-CONICET), Av. Angel Gallardo 470, (C1405DJR), Buenos Aires, Argentina
| | - Andres Porta
- Museo Argentino de Ciencias Naturales “Bernardino Rivadavia” (MACN-CONICET), Av. Angel Gallardo 470, (C1405DJR), Buenos Aires, Argentina
| | - Ezequiel Mabragaña
- Grupo de Biotaxonomía Morfológica y Molecular de Peces (BIMOPE), Instituto de Investigaciones Marinas y Costeras, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata (CONICET), Dean Funes 3350, (B7600), Mar del Plata, Argentina
| | - Emanuel Grassi
- Instituto Misionero de Biodiversidad (IMiBio), Ruta N12 km 5, (N3370), Puerto Iguazú, Misiones, Argentina
| | - Jorge Palermo
- Departamento de Biología, Facultad de Ciencias Naturales, Universidad Nacional de la Patagonia San Juan Bosco (CONICET), Ruta 259 km 16.4, (9000), Esquel, Chubut, Argentina
- Unidad de Microanálisis y Métodos Físicos en Química Orgánica (UMYMFOR-CONICET), Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, (1428), Buenos Aires, Argentina
| | - Belen Bukowski
- Museo Argentino de Ciencias Naturales “Bernardino Rivadavia” (MACN-CONICET), Av. Angel Gallardo 470, (C1405DJR), Buenos Aires, Argentina
| | - Pablo Tubaro
- Museo Argentino de Ciencias Naturales “Bernardino Rivadavia” (MACN-CONICET), Av. Angel Gallardo 470, (C1405DJR), Buenos Aires, Argentina
| | - Nahuel Schenone
- Centro de Investigaciones Antonia Ramos (CIAR), Fundación Bosques Nativos Argentinos, Camino Balneario s/n, Villa Bonita, Misiones, Argentina
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5
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Wang JD, Wang WZ, Lin ZL, Ali A, Fu HY, Huang MT, Gao SJ, Wang R. DNA Barcoding for Identification of Sugarcane Borers in China. NEOTROPICAL ENTOMOLOGY 2018; 47:362-368. [PMID: 28965311 DOI: 10.1007/s13744-017-0560-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 09/03/2017] [Indexed: 06/07/2023]
Abstract
Sugarcane borers are economically damaging insects with species that vary in distribution patterns both geographically and temporally, and vary based on ecological niche. Currently, identification of sugarcane borers is mostly based on morphological characters. However, morphological identification requires taxonomic expertise. An alternative method to identify sugarcane borers is the use of molecular data. DNA barcoding based on partial cytochrome c oxidase subunit 1 (COI) sequences has proven to be a useful tool for rapid and accurate species determination in many insect taxa. This study was conducted to test the effectiveness of DNA barcodes to discriminate among sugarcane borer species in China. Partial sequences of the COI gene (709 bp) were obtained from six species collected from different geographic areas. Results showed that the pairwise intraspecies genetic distance was < 0.02, whereas the interspecies genetic distance ranged from 0.117 to 0.182. Results from a neighbor-joining tree showed that the six sugarcane borer species were certainly separated. These results suggested that the partial COI sequences had high barcoding resolution in discriminating among sugarcane borer species. Our study emphasized the use of DNA barcodes for identification of the analyzed sugarcane borer species and represents an important step for building a comprehensive barcode library for sugarcane borers in China.
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Affiliation(s)
- J- D Wang
- National Engineering Research Center for Sugarcane, Fujian Agricultural and Forestry Univ, Fuzhou, Fujian, 350002, China.
| | - W- Z Wang
- National Engineering Research Center for Sugarcane, Fujian Agricultural and Forestry Univ, Fuzhou, Fujian, 350002, China
| | - Z- L Lin
- National Engineering Research Center for Sugarcane, Fujian Agricultural and Forestry Univ, Fuzhou, Fujian, 350002, China
| | - A Ali
- National Engineering Research Center for Sugarcane, Fujian Agricultural and Forestry Univ, Fuzhou, Fujian, 350002, China
| | - H- Y Fu
- National Engineering Research Center for Sugarcane, Fujian Agricultural and Forestry Univ, Fuzhou, Fujian, 350002, China
| | - M- T Huang
- National Engineering Research Center for Sugarcane, Fujian Agricultural and Forestry Univ, Fuzhou, Fujian, 350002, China
| | - S- J Gao
- National Engineering Research Center for Sugarcane, Fujian Agricultural and Forestry Univ, Fuzhou, Fujian, 350002, China
| | - R Wang
- College of Forestry, Fujian Agricultural and Forestry Univ, Fuzhou, Fujian, 350002, China.
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6
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Lavinia PD, Núñez Bustos EO, Kopuchian C, Lijtmaer DA, García NC, Hebert PDN, Tubaro PL. Barcoding the butterflies of southern South America: Species delimitation efficacy, cryptic diversity and geographic patterns of divergence. PLoS One 2017; 12:e0186845. [PMID: 29049373 PMCID: PMC5648246 DOI: 10.1371/journal.pone.0186845] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 10/09/2017] [Indexed: 01/26/2023] Open
Abstract
Because the tropical regions of America harbor the highest concentration of butterfly species, its fauna has attracted considerable attention. Much less is known about the butterflies of southern South America, particularly Argentina, where over 1,200 species occur. To advance understanding of this fauna, we assembled a DNA barcode reference library for 417 butterfly species of Argentina, focusing on the Atlantic Forest, a biodiversity hotspot. We tested the efficacy of this library for specimen identification, used it to assess the frequency of cryptic species, and examined geographic patterns of genetic variation, making this study the first large-scale genetic assessment of the butterflies of southern South America. The average sequence divergence to the nearest neighbor (i.e. minimum interspecific distance) was 6.91%, ten times larger than the mean distance to the furthest conspecific (0.69%), with a clear barcode gap present in all but four of the species represented by two or more specimens. As a consequence, the DNA barcode library was extremely effective in the discrimination of these species, allowing a correct identification in more than 95% of the cases. Singletons (i.e. species represented by a single sequence) were also distinguishable in the gene trees since they all had unique DNA barcodes, divergent from those of the closest non-conspecific. The clustering algorithms implemented recognized from 416 to 444 barcode clusters, suggesting that the actual diversity of butterflies in Argentina is 3%-9% higher than currently recognized. Furthermore, our survey added three new records of butterflies for the country (Eurema agave, Mithras hannelore, Melanis hillapana). In summary, this study not only supported the utility of DNA barcoding for the identification of the butterfly species of Argentina, but also highlighted several cases of both deep intraspecific and shallow interspecific divergence that should be studied in more detail.
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Affiliation(s)
- Pablo D. Lavinia
- Museo Argentino de Ciencias Naturales ‘Bernardino Rivadavia’ (MACN-CONICET), Buenos Aires, Argentina
| | - Ezequiel O. Núñez Bustos
- Museo Argentino de Ciencias Naturales ‘Bernardino Rivadavia’ (MACN-CONICET), Buenos Aires, Argentina
| | - Cecilia Kopuchian
- Laboratorio de Biología de la Conservación, Centro de Ecología Aplicada del Litoral (CECOAL-CONICET), Corrientes, Argentina
| | - Darío A. Lijtmaer
- Museo Argentino de Ciencias Naturales ‘Bernardino Rivadavia’ (MACN-CONICET), Buenos Aires, Argentina
| | - Natalia C. García
- Museo Argentino de Ciencias Naturales ‘Bernardino Rivadavia’ (MACN-CONICET), Buenos Aires, Argentina
| | - Paul D. N. Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Pablo L. Tubaro
- Museo Argentino de Ciencias Naturales ‘Bernardino Rivadavia’ (MACN-CONICET), Buenos Aires, Argentina
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Chakraborty M, Dhar B, Ghosh SK. Design of character-based DNA barcode motif for species identification: A computational approach and its validation in fishes. Mol Ecol Resour 2017; 17:1359-1370. [PMID: 28332322 DOI: 10.1111/1755-0998.12671] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Revised: 01/26/2017] [Accepted: 03/07/2017] [Indexed: 11/29/2022]
Abstract
The DNA barcodes are generally interpreted using distance-based and character-based methods. The former uses clustering of comparable groups, based on the relative genetic distance, while the latter is based on the presence or absence of discrete nucleotide substitutions. The distance-based approach has a limitation in defining a universal species boundary across the taxa as the rate of mtDNA evolution is not constant throughout the taxa. However, character-based approach more accurately defines this using a unique set of nucleotide characters. The character-based analysis of full-length barcode has some inherent limitations, like sequencing of the full-length barcode, use of a sparse-data matrix and lack of a uniform diagnostic position for each group. A short continuous stretch of a fragment can be used to resolve the limitations. Here, we observe that a 154-bp fragment, from the transversion-rich domain of 1367 COI barcode sequences can successfully delimit species in the three most diverse orders of freshwater fishes. This fragment is used to design species-specific barcode motifs for 109 species by the character-based method, which successfully identifies the correct species using a pattern-matching program. The motifs also correctly identify geographically isolated population of the Cypriniformes species. Further, this region is validated as a species-specific mini-barcode for freshwater fishes by successful PCR amplification and sequencing of the motif (154 bp) using the designed primers. We anticipate that use of such motifs will enhance the diagnostic power of DNA barcode, and the mini-barcode approach will greatly benefit the field-based system of rapid species identification.
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Affiliation(s)
- Mohua Chakraborty
- Department of Biotechnology, Assam University, Silchar, Assam, India
| | - Bishal Dhar
- Department of Biotechnology, Assam University, Silchar, Assam, India
| | - Sankar Kumar Ghosh
- Department of Biotechnology, Assam University, Silchar, Assam, India.,University of Kalyani, Kalyani, West Bengal, India
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Rach J, Bergmann T, Paknia O, DeSalle R, Schierwater B, Hadrys H. The marker choice: Unexpected resolving power of an unexplored CO1 region for layered DNA barcoding approaches. PLoS One 2017; 12:e0174842. [PMID: 28406914 PMCID: PMC5390999 DOI: 10.1371/journal.pone.0174842] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 03/16/2017] [Indexed: 01/13/2023] Open
Abstract
The potential of DNA barcoding approaches to identify single species and characterize species compositions strongly depends on the marker choice. The prominent “Folmer region”, a 648 basepair fragment at the 5’ end of the mitochondrial CO1 gene, has been traditionally applied as a universal DNA barcoding region for metazoans. In order to find a suitable marker for biomonitoring odonates (dragonflies and damselflies), we here explore a new region of the CO1 gene (CO1B) for DNA barcoding in 51 populations of 23 dragonfly and damselfly species. We compare the “Folmer region”, the mitochondrial ND1 gene (NADH dehydrogenase 1) and the new CO1 region with regard to (i) speed and reproducibility of sequence generation, (ii) levels of homoplasy and (iii) numbers of diagnostic characters for discriminating closely related sister taxa and populations. The performances of the gene regions regarding these criteria were quite different. Both, the amplification of CO1B and ND1 was highly reproducible and CO1B showed the highest potential for discriminating sister taxa at different taxonomic levels. In contrast, the amplification of the “Folmer region” using the universal primers was difficult and the third codon positions of this fragment have experienced nucleotide substitution saturation. Most important, exploring this new barcode region of the CO1 gene identified a higher discriminating power between closely related sister taxa. Together with the design of layered barcode approaches adapted to the specific taxonomic “environment”, this new marker will further enhance the discrimination power at the species level.
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Affiliation(s)
- Jessica Rach
- ITZ, Ecology & Evolution, TiHo Hannover, Hannover, D-30559, Germany
| | - Tjard Bergmann
- ITZ, Ecology & Evolution, TiHo Hannover, Hannover, D-30559, Germany
| | - Omid Paknia
- ITZ, Ecology & Evolution, TiHo Hannover, Hannover, D-30559, Germany
| | - Rob DeSalle
- Sackler Institute of Comparative Genomics, American Museum of Natural History, New York, NY 10024, United States of America
| | - Bernd Schierwater
- ITZ, Ecology & Evolution, TiHo Hannover, Hannover, D-30559, Germany
- Sackler Institute of Comparative Genomics, American Museum of Natural History, New York, NY 10024, United States of America
| | - Heike Hadrys
- ITZ, Ecology & Evolution, TiHo Hannover, Hannover, D-30559, Germany
- Sackler Institute of Comparative Genomics, American Museum of Natural History, New York, NY 10024, United States of America
- * E-mail:
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Barreira AS, Lijtmaer DA, Tubaro PL. The multiple applications of DNA barcodes in avian evolutionary studies. Genome 2016; 59:899-911. [DOI: 10.1139/gen-2016-0086] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
DNA barcodes of birds are currently available for 41% of known species and for many different geographic areas; therefore, they are a rich data source to answer evolutionary questions. We review studies that have used DNA barcodes to investigate evolutionary processes in birds using diverse approaches. We also review studies that have investigated species in depth where taxonomy and DNA barcodes present inconsistencies. Species that showed low genetic interspecific divergence and lack of reciprocal monophyly either are the result of recent radiation and (or) hybridize, while species with large genetic splits in their COI sequences were determined to be more than one independent evolutionary unit. In addition, we review studies that employed large DNA barcode datasets to study the molecular evolution of mitochondrial genes and the biogeography of islands, continents, and even at a multi-continental scale. These studies showed that DNA barcodes offer high-quality data well beyond their main purpose of serving as a molecular tool for species identification.
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Affiliation(s)
- Ana S. Barreira
- División Ornitología, Museo Argentino de Ciencias Naturales “Bernardino Rivadavia” - CONICET, Avda. Ángel Gallardo 470, Ciudad Autónoma de Buenos Aires, C1405DJR, Argentina
- División Ornitología, Museo Argentino de Ciencias Naturales “Bernardino Rivadavia” - CONICET, Avda. Ángel Gallardo 470, Ciudad Autónoma de Buenos Aires, C1405DJR, Argentina
| | - Darío A. Lijtmaer
- División Ornitología, Museo Argentino de Ciencias Naturales “Bernardino Rivadavia” - CONICET, Avda. Ángel Gallardo 470, Ciudad Autónoma de Buenos Aires, C1405DJR, Argentina
- División Ornitología, Museo Argentino de Ciencias Naturales “Bernardino Rivadavia” - CONICET, Avda. Ángel Gallardo 470, Ciudad Autónoma de Buenos Aires, C1405DJR, Argentina
| | - Pablo L. Tubaro
- División Ornitología, Museo Argentino de Ciencias Naturales “Bernardino Rivadavia” - CONICET, Avda. Ángel Gallardo 470, Ciudad Autónoma de Buenos Aires, C1405DJR, Argentina
- División Ornitología, Museo Argentino de Ciencias Naturales “Bernardino Rivadavia” - CONICET, Avda. Ángel Gallardo 470, Ciudad Autónoma de Buenos Aires, C1405DJR, Argentina
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10
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Bilgin R, Ebeoğlu N, İnak S, Kırpık MA, Horns JJ, Şekercioğlu ÇH. DNA Barcoding of Birds at a Migratory Hotspot in Eastern Turkey Highlights Continental Phylogeographic Relationships. PLoS One 2016; 11:e0154454. [PMID: 27304877 PMCID: PMC4909268 DOI: 10.1371/journal.pone.0154454] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 04/13/2016] [Indexed: 11/25/2022] Open
Abstract
The combination of habitat loss, climate change, direct persecution, introduced species and other components of the global environmental crisis has resulted in a rapid loss of biodiversity, including species, population and genetic diversity. Birds, which inhabit a wide spectrum of different habitat types, are particularly sensitive to and indicative of environmental changes. The Caucasus endemic bird area, part of which covers northeastern Turkey, is one of the world’s key regions harboring a unique bird community threatened with habitat loss. More than 75% of all bird species native to Turkey have been recorded in this region, in particular along the Kars-Iğdır migratory corridor, stopover, wintering and breeding sites along the Aras River, whose wetlands harbor at least 264 bird species. In this study, DNA barcoding technique was used for evaluating the genetic diversity of land bird species of Aras River Bird Paradise at the confluence of Aras River and Iğdır Plains key biodiversity areas. Seventy three COI sequences from 33 common species and 26 different genera were newly generated and used along with 301 sequences that were retrieved from the Barcoding of Life Database (BOLD). Using the sequences obtained in this study, we made global phylogeographic comparisons to define four categories of species, based on barcoding suitability, intraspecific divergence and taxonomy. Our findings indicate that the landbird community of northeastern Turkey has a genetical signature mostly typical of northern Palearctic bird communities while harboring some unique variations. The study also provides a good example of how DNA barcoding can build upon its primary mission of species identification and use available data to integrate genetic variation investigated at the local scale into a global framework. However, the rich bird community of the Aras River wetlands is highly threatened with the imminent construction of the Tuzluca Dam by the government.
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Affiliation(s)
- Raşit Bilgin
- Institute of Environmental Sciences, Boğaziçi University, Bebek, 34342, Istanbul, Turkey
- * E-mail:
| | - Nadin Ebeoğlu
- Institute of Environmental Sciences, Boğaziçi University, Bebek, 34342, Istanbul, Turkey
| | - Sedat İnak
- Kafkas University, Faculty of Science, Department of Biology, TR-36100 Kars, Turkey
| | - Mehmet Ali Kırpık
- Kafkas University, Faculty of Science, Department of Biology, TR-36100 Kars, Turkey
| | - Joshua J. Horns
- University of Utah, Department of Biology 257 S 1400 E, Salt Lake City, UT 84112, United States of America
| | - Çağan H. Şekercioğlu
- University of Utah, Department of Biology 257 S 1400 E, Salt Lake City, UT 84112, United States of America
- College of Sciences, Koç University, Rumelifeneri, Istanbul 34450, Turkey
- KuzeyDoğa Derneği, Ortakapı Mah. Șehit Yusuf Cad., No: 93/1, 36100 Kars, Turkey
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11
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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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12
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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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13
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Lavinia PD, Escalante P, García NC, Barreira AS, Trujillo-Arias N, Tubaro PL, Naoki K, Miyaki CY, Santos FR, Lijtmaer DA. Continental-scale analysis reveals deep diversification within the polytypic Red-crowned Ant Tanager (Habia rubica, Cardinalidae). Mol Phylogenet Evol 2015; 89:182-93. [DOI: 10.1016/j.ympev.2015.04.018] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 04/11/2015] [Accepted: 04/20/2015] [Indexed: 02/07/2023]
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14
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Reddy S. What’s missing from avian global diversification analyses? Mol Phylogenet Evol 2014; 77:159-65. [DOI: 10.1016/j.ympev.2014.04.023] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2013] [Revised: 04/18/2014] [Accepted: 04/18/2014] [Indexed: 11/25/2022]
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15
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Saitoh T, Sugita N, Someya S, Iwami Y, Kobayashi S, Kamigaichi H, Higuchi A, Asai S, Yamamoto Y, Nishiumi I. DNA barcoding reveals 24 distinct lineages as cryptic bird species candidates in and around the Japanese Archipelago. Mol Ecol Resour 2014; 15:177-86. [PMID: 24835119 DOI: 10.1111/1755-0998.12282] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 05/01/2014] [Accepted: 05/05/2014] [Indexed: 11/29/2022]
Abstract
DNA barcoding using a partial region (648 bp) of the cytochrome c oxidase I (COI) gene is a powerful tool for species identification and has revealed many cryptic species in various animal taxa. In birds, cryptic species are likely to occur in insular regions like the Japanese Archipelago due to the prevention of gene flow by sea barriers. Using COI sequences of 234 of the 251 Japanese-breeding bird species, we established a DNA barcoding library for species identification and estimated the number of cryptic species candidates. A total of 226 species (96.6%) had unique COI sequences with large genetic divergence among the closest species based on neighbour-joining clusters, genetic distance criterion and diagnostic substitutions. Eleven cryptic species candidates were detected, with distinct intraspecific deep genetic divergences, nine lineages of which were geographically separated by islands and straits within the Japanese Archipelago. To identify Japan-specific cryptic species from trans-Paleartic birds, we investigated the genetic structure of 142 shared species over an extended region covering Japan and Eurasia; 19 of these species formed two or more clades with high bootstrap values. Excluding six duplicated species from the total of 11 species within the Japanese Archipelago and 19 trans-Paleartic species, we identified 24 species that were cryptic species candidates within and surrounding the Japanese Archipelago. Repeated sea level changes during the glacial and interglacial periods may be responsible for the deep genetic divergences of Japanese birds in this insular region, which has led to inconsistencies in traditional taxonomies based on morphology.
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Affiliation(s)
- Takema Saitoh
- Division of Natural History, Yamashina Institute for Ornithology, 115 Konoyama, Abiko, Chiba, 270-1145, Japan
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16
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Chakraborty M, Ghosh SK. An assessment of the DNA barcodes of Indian freshwater fishes. Gene 2014; 537:20-8. [DOI: 10.1016/j.gene.2013.12.047] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Revised: 12/13/2013] [Accepted: 12/18/2013] [Indexed: 11/17/2022]
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17
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Milá B, Tavares ES, Muñoz Saldaña A, Karubian J, Smith TB, Baker AJ. A trans-Amazonian screening of mtDNA reveals deep intraspecific divergence in forest birds and suggests a vast underestimation of species diversity. PLoS One 2012; 7:e40541. [PMID: 22815761 PMCID: PMC3398903 DOI: 10.1371/journal.pone.0040541] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Accepted: 06/11/2012] [Indexed: 11/19/2022] Open
Abstract
The Amazonian avifauna remains severely understudied relative to that of the temperate zone, and its species richness is thought to be underestimated by current taxonomy. Recent molecular systematic studies using mtDNA sequence reveal that traditionally accepted species-level taxa often conceal genetically divergent subspecific lineages found to represent new species upon close taxonomic scrutiny, suggesting that intraspecific mtDNA variation could be useful in species discovery. Surveys of mtDNA variation in Holarctic species have revealed patterns of variation that are largely congruent with species boundaries. However, little information exists on intraspecific divergence in most Amazonian species. Here we screen intraspecific mtDNA genetic variation in 41 Amazonian forest understory species belonging to 36 genera and 17 families in 6 orders, using 758 individual samples from Ecuador and French Guiana. For 13 of these species, we also analyzed trans-Andean populations from the Ecuadorian Chocó. A consistent pattern of deep intraspecific divergence among trans-Amazonian haplogroups was found for 33 of the 41 taxa, and genetic differentiation and genetic diversity among them was highly variable, suggesting a complex range of evolutionary histories. Mean sequence divergence within families was the same as that found in North American birds (13%), yet mean intraspecific divergence in Neotropical species was an order of magnitude larger (2.13% vs. 0.23%), with mean distance between intraspecific lineages reaching 3.56%. We found no clear relationship between genetic distances and differentiation in plumage color. Our results identify numerous genetically and phenotypically divergent lineages which may result in new species-level designations upon closer taxonomic scrutiny and thorough sampling, although lineages in the tropical region could be older than those in the temperate zone without necessarily representing separate species. In-depth phylogeographic surveys are urgently needed to avoid underestimating tropical diversity, and the use of mtDNA markers can be instrumental in identifying and prioritizing taxa for species discovery.
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Affiliation(s)
- Borja Milá
- National Museum of Natural Sciences, Spanish Research Council (CSIC), Madrid, Spain.
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18
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Lijtmaer DA, Kerr KCR, Stoeckle MY, Tubaro PL. DNA barcoding birds: from field collection to data analysis. Methods Mol Biol 2012; 858:127-152. [PMID: 22684955 DOI: 10.1007/978-1-61779-591-6_7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
As of February 2011, COI DNA barcode sequences (a 648-bp segment of the 5' end of the mitochondrial gene cytochrome c oxidase I, the standard DNA barcode for animals) have been collected from over 23,000 avian specimens representing 3,800 species, more than one-third of the world's avifauna. Here, we detail the methodology for obtaining DNA barcodes from birds, covering the entire process from field collection to data analysis. We emphasize key aspects of the process and describe in more detail those that are particularly relevant in the case of birds. We provide elemental information about collection of specimens, detailed protocols for DNA extraction and PCR, and basic aspects of sequencing methodology. In particular, we highlight the primer pairs and thermal cycling profiles associated with successful amplification and sequencing from a broad range of avian species. Finally, we succinctly review the methodology for data analysis, including the detection of errors (such as contamination, misidentifications, or amplification of pseudogenes), assessment of species resolution, detection of divergent intraspecific lineages, and identification of unknown specimens.
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