<scp>DNA</scp> barcoding reveals novel insights into pterygophagy and prey selection in distichodontid fishes (Characiformes: Distichodontidae)

Arroyave, Jairo

doi:10.1002/ece3.1321

Cited by 13 publications

(3 citation statements)

References 31 publications

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“…DNA barcoding was conducted using COI sequences blasted in the GenBank and BOLD online databases with a threshold of similarity higher than 98% [42]. Specimens would be re-examined if any conflict exists between morphological and molecular identification.…”

Section: Methodsmentioning

confidence: 99%

DNA barcoding of coastal ray-finned fishes in Vietnam

et al. 2019

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DNA barcoding based on a fragment of the cytochrome c oxidase subunit I (COI) gene is widely applied in species identification and biodiversity studies. The aim of this study was to establish a comprehensive barcoding database of coastal ray-finned fishes in Vietnam. A total of 3,638 specimens were collected from fish landing sites in northern, central and southern Vietnam. Seven hundred and sixty-five COI sequences of ray-finned fishes were generated, belonging to 458 species, 273 genera, 113 families and 43 orders. A total of 59 species were newly recorded in Vietnam and sequences of six species were new to the Genbank and BOLD online databases. Only 32 species cannot be annotated to species level because difficulty in morphological identifications and their Kimura-2-Parameter (K2P) genetic distances to most similar sequences were more than 2%. Moreover, intra-specific genetic distances in some species are also higher than 2%, implying the existence of putative cryptic species. The mean K2P genetic distances within species, genera, families, orders and classes were 0.34%, 12.14%, 17.39%, 21.42%, and 24.80, respectively. Species compositions are quite different with only 16 common species among northern, central and southern Vietnam. This may attribute to multiple habitats and environmental factors across the 3,260 km Vietnamese coastline. Our results confirmed that DNA barcoding is an efficient and reliable tool for coastal fish identification in Vietnam, and also established a reliable DNA barcode reference library for these fishes. DNA barcodes will contribute to future efforts to achieve better monitoring, conservation, and management of fisheries in Vietnam.

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Section: Methodsmentioning

confidence: 99%

DNA barcoding of coastal ray-finned fishes in Vietnam

et al. 2019

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“…g . fish fillets and caviar), stomach contents as well as fish larvae and eggs (Desalle & Amato, ; Carreon‐Martinez et al , ; Carvalho et al , 2011 a ; Ko et al , ; Arroyave & Stiassny, ; Loh et al , ). For instance, Loh et al () developed and applied DNA barcoding to identify 14 of the 16 species inhabiting the Brisbane River (Australia), including a quantitative (q)PCR assay for species‐specific detection and quantification.…”

Section: Introductionmentioning

confidence: 99%

DNA barcoding and morphological identification of neotropical ichthyoplankton from the Upper Paraná and São Francisco

Becker

Sales

Santos

et al. 2015

Journal of Fish Biology

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The identification of fish larvae from two neotropical hydrographic basins using traditional morphological taxonomy and DNA barcoding revealed no conflicting results between the morphological and barcode identification of larvae. A lower rate (25%) of correct morphological identification of eggs as belonging to migratory or non-migratory species was achieved. Accurate identification of ichthyoplankton by DNA barcoding is an important tool for fish reproductive behaviour studies, correct estimation of biodiversity by detecting eggs from rare species, as well as defining environmental and management strategies for fish conservation in the neotropics.

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“…This observation reinforces the idea that more sequences of fish species must be deposited in databases, especially in river basins with rich fish fauna as the Upper Paraná River. Another positive aspect is that, compared with DNA barcoding (Arroyave and Stiassny 2014, Becker et al 2015, Frantine-Silva et al 2015, our method can trigger significant advances in the quality of ecological studies in fish, as observed in some recent studies with metabarcoding (Guillerault et al 2017, Maggia et al 2017, Mariac et al 2018, Barbato et al 2019 and, mainly, to ensure significant reduction in labor time and cost per specimen reaching 80% of reduction (Shokralla et al 2015). Despite some differences in obtaining DNA samples, both environmental DNA (eDNA) and DNA metabarcoding from bulk samples are subject to false negatives and false positives (Ficetola Gentile et al 2015Gentile et al , 2016Divoll et al 2018).…”

Section: Species Identificationmentioning

confidence: 99%

DNA metabarcoding of Neotropical ichthyoplankton: Enabling high accuracy with lower cost

Nobile¹,

Freitas‐Souza²,

Ruiz‐Ruano³

et al. 2019

MBMG

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Knowledge of ichthyoplankton dynamics is extremely important for conservation management as it can provide information about preferential spawning sites, reproductive period, migratory routes and recruitment success, which can be used to guide management and conservation efforts. However, identification of the eggs and larvae of Neotropical freshwater fish is a difficult task. DNA barcodes have emerged as an alternative and highly accurate approach for species identification, but DNA barcoding can be time-consuming and costly. To solve this problem, we aimed to develop a simple protocol based on DNA metabarcoding, to investigate whether it is possible to detect and quantify all species present in a pool of organisms. To do this, 230 larvae were cut in half, one half was sequenced by the Sanger technique and the other half was used to compose six arrays with a pool of larvae that were sequenced using a next-generation technique (NGS). The results of the Sanger sequencing allowed the identification of almost all larvae at species level, and the results from NGS showed high accuracy in species detection, ranging from 83% to 100%, with an average of 95% in all samples. No false positives were detected. The frequency of organisms in the two methods was positively correlated (Pearson), with low variation among species. In conclusion, this protocol represents a considerable advance in ichthyoplankton studies, allowing a rapid, cost-effective, quali-quantitative approach that improves the accuracy of identification.

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DNA barcoding reveals novel insights into pterygophagy and prey selection in distichodontid fishes (Characiformes: Distichodontidae)

Cited by 13 publications

References 31 publications

DNA barcoding of coastal ray-finned fishes in Vietnam

DNA barcoding of coastal ray-finned fishes in Vietnam

DNA barcoding and morphological identification of neotropical ichthyoplankton from the Upper Paraná and São Francisco

DNA metabarcoding of Neotropical ichthyoplankton: Enabling high accuracy with lower cost

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