DNA Barcoding and Elucidation of Cryptic Diversity in Thrips (Thysanoptera)

Rebijith, K. B.; Asokan, R.; Krishna, V.; Ranjitha, H. H.; Kumar, N. K. Krishna; Ramamurthy, V. V.

doi:10.1653/024.097.0407

Cited by 36 publications

(45 citation statements)

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“…g . thrips: 0.0 to 7.91% and 8.65% to 31.15% [84]; mosquitoes: 0–1.67% and 2.3–21.8% [85]), although the greater intraspecific diversity showed some overlap with interspecific divergence. Hebert et al .…”

Section: Discussionmentioning

confidence: 99%

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Species Delimitation and Phylogenetic Relationships in Ectobiid Cockroaches (Dictyoptera, Blattodea) from China

Che

Gui

et al. 2017

PLoS ONE

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We collected Ectobiidae cockroach specimens from 44 locations in the south of the Yangtze valley. We obtained 297 COI sequences specimens and carried out phylogenetic and divergence dating analyses, as well as species delimitation analysis using a General Mixed Yule Coalescent (GMYC) framework. The intraspecific and interspecific sequence divergence in Ectobiidae cockroaches ranged from 0.0 to 7.0% and 4.6 to 30.8%, respectively. GMYC analysis resulted in 53 (confidence interval: 37–65) entities (likelihood ratio = 103.63) including 14 downloaded species. The COI GMYC groups partly corresponded to the ectobiid species and 52 ectobiid species were delimited successfully based on the combination of GMYC result with morphological information. We used the molecular data and 6 cockroach fossil calibrations to obtain a preliminary estimate of the timescale of ectobiid evolution. The major subfamilies in the group were found to have diverged between ~125–110 Ma, and morphospecies pairs were found to have diverged ~10 or more Ma.

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Section: Discussionmentioning

confidence: 99%

“…Rebijith et al . [84] reported that the intraspecific and intrageneric distances of COI barcode sequence for 151 thrip species ranged from 0.0 to 7.91% and 8.65% to 31.15% respectively. Both Meyer & Paulay [88] and Wieners et al .…”

Section: Discussionmentioning

confidence: 99%

Species Delimitation and Phylogenetic Relationships in Ectobiid Cockroaches (Dictyoptera, Blattodea) from China

Che

Gui

et al. 2017

PLoS ONE

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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%

“…Reflecting the ease of recovering sequence information, and access to refined analytical tools, the discovery of new cryptic species is now commonplace in many animal groups. Cryptic species have important implications for taxonomic, evolutionary, and biodiversity studies, but their presence in pest taxa also has economic and regulatory implications (Piffaretti et al 2013;Rebijith et al 2014). Several studies have considered the impact of cryptic species on pest management (Frewin et al 2014;Ovalle et al 2014), biological control strategies (Derocles et al 2015), the detection of invasive species (Blacket et al 2015;Li et al 2015), and quarantine inspections (Kang et al 2015).…”

Section: Cryptic Speciesmentioning

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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“…Because the method uses DNA instead of morphological characteristics, it can be equally well used for identification of taxa at all life stages . Unlike traditional morphological identification, DNA barcoding also enables the identification of cryptic insect pest lineages . However, although barcodes exist for well over 2 million different arthropod species, the method is limited by the fact that it can only identify specimens for which pre‐existing reference barcode sequences are readily available …”

Section: Introductionmentioning

confidence: 99%

From laboratory to point of entry: development and implementation of a loop‐mediated isothermal amplification (LAMP)‐based genetic identification system to prevent introduction of quarantine insect species

Blaser

Diem

Felten

et al. 2018

Pest Management Science

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BACKGROUNDRapid genetic on‐site identification methods at points of entry, such as seaports and airports, have the potential to become important tools to prevent the introduction and spread of economically harmful pest species that are unintentionally transported by the global trade of plant commodities. This paper reports the development and evaluation of a loop‐mediated isothermal amplification (LAMP)‐based identification system to prevent introduction of the three most frequently encountered regulated quarantine insect species groups at Swiss borders, Bemisia tabaci, Thrips palmi and several regulated fruit flies of the genera Bactrocera and Zeugodacus.RESULTSThe LAMP primers were designed to target a fragment of the mitochondrial cytochrome c oxidase subunit I gene and were generated based on publicly available DNA sequences. Laboratory evaluations analysing 282 insect specimens suspected to be quarantine organisms revealed an overall test efficiency of 99%. Additional on‐site evaluation at a point of entry using 37 specimens performed by plant health inspectors with minimal laboratory training resulted in an overall test efficiency of 95%. During both evaluation rounds, there were no false‐positives and the observed false‐negatives were attributable to human‐induced manipulation errors. To overcome the possibility of accidental introduction of pests as a result of rare false‐negative results, samples yielding negative results in the LAMP method were also subjected to DNA barcoding.CONCLUSIONOur LAMP assays reliably differentiated between the tested regulated and non‐regulated insect species within <1 h. Hence, LAMP assays represent suitable tools for rapid on‐site identification of harmful pests, which might facilitate an accelerated import control process for plant commodities. © 2018 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

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DNA Barcoding and Elucidation of Cryptic Diversity in Thrips (Thysanoptera)

Cited by 36 publications

References 50 publications

Species Delimitation and Phylogenetic Relationships in Ectobiid Cockroaches (Dictyoptera, Blattodea) from China

Species Delimitation and Phylogenetic Relationships in Ectobiid Cockroaches (Dictyoptera, Blattodea) from China

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

From laboratory to point of entry: development and implementation of a loop‐mediated isothermal amplification (LAMP)‐based genetic identification system to prevent introduction of quarantine insect species

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