DNA barcoding for identification of sand fly species (Diptera: Psychodidae) from leishmaniasis-endemic areas of Peru

Nzelu, Chukwunonso O.; Cáceres, Abraham G.; Arrunátegui-Jiménez, Martín J.; Lañas-Rosas, Máximo F.; Yañez-Trujillano, Henrry H.; Luna-Caipo, Deysi V.; Holguín-Mauricci, Carlos E.; Katakura, Ken; Hashiguchi, Yoshihisa; Kato, Hirotomo

doi:10.1016/j.actatropica.2015.02.003

Cited by 55 publications

(56 citation statements)

References 45 publications

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“…For example, 2% intraspecific divergence may indicate the existence of hidden species in Lepidoptera [11, 74]. However, within Diptera, this level of divergence only represents an intraspecific difference [75–77]. In the suborder Heteroptera, threshold value of 2.2% has been applied for DNA barcode based species delimitation [78–79].…”

Section: Discussionmentioning

confidence: 99%

Cryptic diversity of the subfamily Calaphidinae (Hemiptera: Aphididae) revealed by comprehensive DNA barcoding

Lee

Kanturski

et al. 2017

PLoS ONE

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Aphids are a species rich group comprising many important pests. However, species identification can be very difficult for aphids due to their morphological ambiguity. DNA barcoding has been widely adopted for rapid and reliable species identification as well as cryptic species detection. In this study, we investigated cryptic diversity in the subfamily Calaphidinae (Hemiptera: Aphididae) based on 899 sequences of cytochrome c oxidase I (COI) for 115 morphospecies (78 species collected in this study and sequences of 73 species downloaded from Genbank). Among these 115 morphospecies, DNA barcoding results of 90 (78.3%) species were identical to results of morphological identification. However, 25 (21.7%) morphospecies showed discrepancies between DNA barcoding and traditional taxonomy. Among these 25 discordances, a total of 15 cryptic species were identified from 12 morphospecies. We also found three morphologically distinct species pairs that sharing DNA barcoding. Based on molecular operational taxonomic unit (MOTU) estimation, we discussed on species delimitation threshold value for these taxa. Our findings confirm that Calaphidinae has high cryptic diversity even though aphids are relatively well-studied.

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Section: Discussionmentioning

confidence: 99%

Cryptic diversity of the subfamily Calaphidinae (Hemiptera: Aphididae) revealed by comprehensive DNA barcoding

Lee

Kanturski

et al. 2017

PLoS ONE

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“…However, a fixed threshold of COI sequences is not appropriate for all taxonomic groups. In insects for instance, a 2% threshold provides effective identification at the species level of Ephemeroptera (Schmidt et al 2015;Webb et al 2012;Zhou et al 2010), Lepidoptera (Zahiri et al 2014) and Trichoptera (Zhou et al 2016), while a 2.2% threshold appears appropriate for Heteroptera (Knebelsberger et al 2014), 2.5% for aquatic beetles (Monaghan et al 2005), and >3% for various dipteran groups (Nzelu et al 2015;Renaud et al 2012). Furthermore, an average threshold of 4-5% appears appropriate for most Chironomidae (Lin et al 2015;Meier et al 2015), even if a 7% threshold has been reported for closely related species in this family (Carew & Hoffmann 2015).…”

Section: Dna Barcodes and Morphospeciesmentioning

confidence: 99%

DNA barcodes and morphology reveal unrecognized species in Chironomidae (Diptera)

Stur

Ekrem

2018

Insect Syst. Evol.

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For over a decade, DNA barcoding has proven an effective modern tool in taxonomy, evolutionary biology and biodiversity research. Many new species have been discovered and described with DNA barcodes as part of their diagnostic features. Using DNA barcodes, we uncovered a number of potential species within the Tanytarsus curticornis and Tanytarsus heusdensis species complexes (Diptera: Chironomidae) and detected morphological differences a posteriori that support the description of new species. Unusually large intraspecific divergence in COI p-distance (up to 10%) was observed for two species complexes. In total, eight species new to science are described and figured: T. adustus sp. n., T. heberti sp. n., T. madeiraensis sp. n., T. pseudoheusdensis sp. n., T. songi sp. n., T. thomasi sp. n., T. tongmuensis sp. n. and T. wangi sp. n.. Tanytarsus reei and T. tamaoctavus are redescribed, and T. tusimatneous is listed as a new junior synonym of T. tamaduodecimus. The diagnostic characters of the remaining species of the complexes are discussed. Keys to males and pupae are given.

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“…Molecular methods based on various genetic markers have been developed to overcome this issue (Depaquit 2014). So far, two techniques have been mainly used for molecular identifications of sand flies: the polymerase chain reaction-restriction fragment-length polymorphism (PCR-RFLP; Aransay et al 1999;Terayama et al 2008;Latrofa et al 2012;Tiwary et al 2012;Minter et al 2013) and DNA barcoding (Kr€ uger et al 2011;Kumar et al 2012;Contreras Guti errez et al 2014;Al-Ajmi et al 2015;Maia et al 2015;Nzelu et al 2015;Romero-Ricardo et al 2016). DNA barcoding consists in the sequencing of a short standard DNA marker for the taxonomic assignment of a sample by looking for the closest match in a reference database (Hebert et al 2003a).…”

Section: Introductionmentioning

confidence: 99%

“…Here, the reliability of DNA metabarcoding to identify sand flies fly species contained in bulk samples is assessed. The current standard barcode for animals is a c. 650-bp portion of the mitochondrial cytochrome c oxidase subunit 1 gene (COI) which was already proved useful for the identification of Neotropical sand flies (Contreras Guti errez et al 2014;Nzelu et al 2015;Romero-Ricardo et al 2016). The standard COI barcode is however not well suited for metabarcoding applications.…”

Section: Introductionmentioning

confidence: 99%

Vector soup: high‐throughput identification of Neotropical phlebotomine sand flies using metabarcoding

Kocher

Gantier²,

Gaborit

et al. 2016

Molecular Ecology Resources

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Phlebotomine sand flies are haematophagous dipterans of primary medical importance. They represent the only proven vectors of leishmaniasis worldwide and are involved in the transmission of various other pathogens. Studying the ecology of sand flies is crucial to understand the epidemiology of leishmaniasis and further control this disease. A major limitation in this regard is that traditional morphological-based methods for sand fly species identifications are time-consuming and require taxonomic expertise. DNA metabarcoding holds great promise in overcoming this issue by allowing the identification of multiple species from a single bulk sample. Here, we assessed the reliability of a short insect metabarcode located in the mitochondrial 16S rRNA for the identification of Neotropical sand flies, and constructed a reference database for 40 species found in French Guiana. Then, we conducted a metabarcoding experiment on sand flies mixtures of known content and showed that the method allows an accurate identification of specimens in pools. Finally, we applied metabarcoding to field samples caught in a 1-ha forest plot in French Guiana. Besides providing reliable molecular data for species-level assignations of phlebotomine sand flies, our study proves the efficiency of metabarcoding based on the mitochondrial 16S rRNA for studying sand fly diversity from bulk samples. The application of this high-throughput identification procedure to field samples can provide great opportunities for vector monitoring and eco-epidemiological studies.

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DNA barcoding for identification of sand fly species (Diptera: Psychodidae) from leishmaniasis-endemic areas of Peru

Cited by 55 publications

References 45 publications

Cryptic diversity of the subfamily Calaphidinae (Hemiptera: Aphididae) revealed by comprehensive DNA barcoding

Cryptic diversity of the subfamily Calaphidinae (Hemiptera: Aphididae) revealed by comprehensive DNA barcoding

DNA barcodes and morphology reveal unrecognized species in Chironomidae (Diptera)

Vector soup: high‐throughput identification of Neotropical phlebotomine sand flies using metabarcoding

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