Half of the European fruit fly species barcoded (Diptera, Tephritidae); a feasibility test for molecular identification

Smit, John; Reijnen, Bastian T.; Stokvis, Frank R.

doi:10.3897/zookeys.365.5819

Cited by 39 publications

(36 citation statements)

References 43 publications

(62 reference statements)

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“…Conversely, a high level of correspondence at the species level is observed between morphology and molecular species limits in the tree-based approach in the present study. The performance of DNA-based specimen identification in Diptera using COI differs greatly in the literature, which varies from less than 50% to near 100% congruence levels (Cywinska et al 2006, Smith et al 2006, Whitworth et al 2007, Rivera and Currie 2009, Meiklejohn et al 2012, Renaud et al 2012, Smit et al 2013, Contrearas et al 2014). In most of the studies, identification success rose upon relaxing the bootstrap requirement.…”

Section: Discussionmentioning

confidence: 99%

Mosquito species (Diptera, Culicidae) in three ecosystems from the Colombian Andes: identification through DNA barcoding and adult morphology

Rozo-Lopez¹,

Mengual²

2015

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Colombia, one of the world’s megadiverse countries, has a highly diverse mosquito fauna and a high prevalence of mosquito-borne diseases. In order to provide relevant information about the diversity and taxonomy of mosquito species in Colombia and to test the usefulness of DNA barcodes, mosquito species collected at different elevations in the departments of Antioquia and Caldas were identified combining adult morphology and barcode sequences. A total of 22 mosquito species from eight genera were identified using these combined techniques. We generated 77 barcode sequences with 16 species submitted as new country records for public databases. We examined the usefulness of DNA barcodes to discriminate mosquito species from the Neotropics by compiling 1,292 sequences from a total of 133 species and using the tree-based methods of neighbor-joining and maximum likelihood. Both methodologies provided similar results by resolving 105 species of mosquitoes separated into distinct clusters. This study shows the importance of combining classic morphological methodologies with molecular tools to accurately identify mosquitoes from Colombia.

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Section: Discussionmentioning

confidence: 99%

Mosquito species (Diptera, Culicidae) in three ecosystems from the Colombian Andes: identification through DNA barcoding and adult morphology

Rozo-Lopez¹,

Mengual²

2015

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“…DNA barcoding has a strong track record in delivering species-level identifications for the five insect orders with the most pest species-Coleoptera (Woodcock et al 2013;Rougerie et al 2015), Diptera (Nagy et al 2013;Smit et al 2013), Hemiptera (Park et al 2011b;Raupach et al 2014), Lepidoptera (Janzen et al 2005;Ashfaq et al 2013), and Thysanoptera (Rebijith et al 2014;Iftikhar et al 2016). For example, 92.2% of 3514 species of European beetles were assigned to a distinct BIN that coincided with a known morphological species, while most of the other species were assigned to two or three BINs, suggesting they represent cryptic species complexes (Hendrich et al 2015).…”

Section: Effectiveness Of Dna Barcodes For Arthropod Identificationmentioning

confidence: 99%

DNA barcodes for bio-surveillance: regulated and economically important arthropod plant pests

Ashfaq

Hebert

2016

Genome

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Many of the arthropod species that are important pests of agriculture and forestry are impossible to discriminate morphologically throughout all of their life stages. Some cannot be differentiated at any life stage. Over the past decade, DNA barcoding has gained increasing adoption as a tool to both identify known species and to reveal cryptic taxa. Although there has not been a focused effort to develop a barcode library for them, reference sequences are now available for 77% of the 409 species of arthropods documented on major pest databases. Aside from developing the reference library needed to guide specimen identifications, past barcode studies have revealed that a significant fraction of arthropod pests are a complex of allied taxa. Because of their importance as pests and disease vectors impacting global agriculture and forestry, DNA barcode results on these arthropods have significant implications for quarantine detection, regulation, and management. The current review discusses these implications in light of the presence of cryptic species in plant pests exposed by DNA barcoding.Key words: species identification, cryptic taxa, invasive species, quarantine, pest management.Résumé : Plusieurs des espèces d'arthropodes qui constituent d'importants ravageurs en agriculture en foresterie sont impossibles à distinguer sur la base morphologique au cours de certains stades de vie. Il est impossible d'en distinguer certains à tous les stades. Au cours de la dernière décennie, l'adoption du codage à barres de l'ADN s'est accrue tant pour l'identification des espèces connues que cryptiques. Bien qu'il n'y ait pas eu d'effort visant à développer une banque de références pour ces espèces, des séquences de référence sont présentement disponibles pour 77 % des 409 espèces d'arthropodes cataloguées parmi les bases de données de ravageurs importants. Outre le développement de la banque de références nécessaire à l'identification des spécimens, les études antérieures ont révélé qu'une portion significative des arthropodes nuisibles sont composés d'un ensemble de taxons apparentés. En raison de leur importance en tant que ravageurs ou vecteurs de maladies ayant un impact global en agriculture et en foresterie, les résultats du codage à barres de ces arthropodes ont des implications importantes en matière de détection, de réglementation et de gestion de quarantaines. Dans cette synthèse, les auteurs discutent des implications à la lumière de la présence d'espèces cryptiques, au sein de ravageurs de plantes, mises au jour grâce au codage à barres de l'ADN. [Traduit par la Rédaction]

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“…; Smit et al . ); however, no studies have evaluated the ability of DNA barcoding for fruit flies identification based on comprehensive analyses of all the public sequences in BOLD and much more new data. In this study, we used Bactrocera , which is the largest genus of Tephritidae, as a case study.…”

Section: Introductionmentioning

confidence: 99%

“…In Diptera, however, the identification success based on COI barcodes was relatively low due to the substantial overlaps in intra-and interspecific divergences (Meier et al 2006;Virgilio et al 2010). Tephritidae has been extensively studied from the perspective of DNA barcoding (Armstrong & Ball 2005;Van Houdt et al 2010;Barr et al 2012;Blacket et al 2012;Virgilio et al 2012;Smit et al 2013); however, no studies have evaluated the ability of DNA barcoding for fruit flies identification based on comprehensive analyses of all the public sequences in BOLD and much more new data. In this study, we used Bactrocera, which is the largest genus of Tephritidae, as a case study.…”

Section: Introductionmentioning

confidence: 99%

Existence of species complex largely reduced barcoding success for invasive species ofTephritidae: a case study inBactroceraspp.

Fan

Jin

Liang

et al. 2014

Molecular Ecology Resources

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Fruit flies in the family Tephritidae are the economically important pests that have many species complexes. DNA barcoding has gradually been verified as an effective tool for identifying species in a wide range of taxonomic groups, and there are several publications on rapid and accurate identification of fruit flies based on this technique; however, comprehensive analyses of large and new taxa for the effectiveness of DNA barcoding for fruit flies identification have been rare. In this study, we evaluated the COI barcode sequences for the diagnosis of fruit flies using 1426 sequences for 73 species of Bactrocera distributed worldwide. Tree-based [neighbour-joining (NJ)]; distance-based, such as Best Match (BM), Best Close Match (BCM) and Minimum Distance (MD); and character-based methods were used to evaluate the barcoding success rates obtained with maintaining the species complex in the data set, treating a species complex as a single taxon unit, and removing the species complex. Our results indicate that the average divergence between species was 14.04% (0.00-25.16%), whereas within a species this was 0.81% (0.00-9.71%); the existence of species complexes largely reduced the barcoding success for Tephritidae, for example relatively low success rates (74.4% based on BM and BCM and 84.8% based on MD) were obtained when the sequences from species complexes were included in the analysis, whereas significantly higher success rates were achieved if the species complexes were treated as a single taxon or removed from the data set - BM (98.9%), BCM (98.5%) and MD (97.5%), or BM (98.1%), BCM (97.4%) and MD (98.2%).

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Half of the European fruit fly species barcoded (Diptera, Tephritidae); a feasibility test for molecular identification

Cited by 39 publications

References 43 publications

Mosquito species (Diptera, Culicidae) in three ecosystems from the Colombian Andes: identification through DNA barcoding and adult morphology

Mosquito species (Diptera, Culicidae) in three ecosystems from the Colombian Andes: identification through DNA barcoding and adult morphology

DNA barcodes for bio-surveillance: regulated and economically important arthropod plant pests

Existence of species complex largely reduced barcoding success for invasive species ofTephritidae: a case study inBactroceraspp.

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