Identification of North Sea molluscs with DNA barcoding

Abstract

Sequence-based specimen identification, known as DNA barcoding, is a common method complementing traditional morphology-based taxonomic assignments. The fundamental resource in DNA barcoding is the availability of a taxonomically reliable sequence database to use as a reference for sequence comparisons. Here, we provide a reference library including 579 sequences of the mitochondrial cytochrome c oxidase subunit I for 113 North Sea mollusc species. We tested the efficacy of this library by simulating a sequence-based specimen identification scenario using Best Match, Best Close Match (BCM) and All Species Barcode (ASB) criteria with three different threshold values. Each identification result was compared with our prior morphology-based taxonomic assignments. Our simulation resulted in 87.7% congruent identifications (93.8% when excluding singletons). The highest number of congruent identifications was obtained with BCM and ASB and a 0.05 threshold. We also compared identifications with genetic clustering (Barcode Index Numbers, BINs) computed by the Barcode of Life Datasystem (BOLD). About 68% of our morphological identifications were congruent with BINs created by BOLD. Forty-nine sequences were clustered in 16 discordant BINs, and these were divided in two classes: sequences from different species clustered in a single BIN and conspecific sequences divided in more BINs. Whereas former incongruences were probably caused by BOLD entries in need of a taxonomic update, the latter incongruences regarded taxa requiring further investigations. These include species with amphi-Atlantic distribution, whose genetic structure should be evaluated over their entire range to produce a reliable sequence-based identification system.

With a little help from DNA barcoding: investigating the diversity of Gastropoda from the Portuguese coast

“…For this reason, O. edwardsii complex was recently the subject of a study using molecular markers (mitochondrial and nuclear) to attempt species delimitation 36 . In addition, in this study we included several species of this genus from other studies, available in GenBank 16 36 38 ( supplementary Table S1 , Fig. 2 ).…”

DNA barcoding of Corydalis, the most taxonomically complicated genus of Papaveraceae

“…DNA barcoding, which uses one or several short standardized DNA regions for species identification (CBOL Plant Working Group, ; Hebert, Cywinska, Ball, & deWaard, ; Kress, Wurdack, Zimmer, Weigt, & Janzen, ), exhibits the outstanding advantage of not being affected by morphological characteristics. This technique has been widely applied for species identification (Barco, Raupach, Laakmann, Neumann, & Knebelsberger, ; Liu, Provan, Gao, & Li, ; Yan et al, ), the discovery of new or cryptic species (Huemer, Karsholt, & Mutanen, ; Liu, Möller, Gao, Zhang, & Li, ; Zemlak, Ward, Connell, Holmes, & Hebert, ), the assessment of biodiversity (Ji et al, ; Lahaye et al, ; Taberlet, Coissac, Pompanon, Brochmann, & Willerslev, ), the characterization of genetic diversity (Sucher & Carles, ; Zhang, Niu, Guo, Wang, & Eaton, ), and the identification of species used in traditional Chinese medicine (Chen et al, ; Yuan et al, ). DNA barcoding has been shown to be an effective method for a variety of applications that involve species identification (Yan et al, ), but its performance in this taxonomically complicated genus has not been evaluated.…”

Comparison of Rapid Biodiversity Assessment of Meiobenthos Using MALDI-TOF MS and Metabarcoding

“…The most commonly applied method is COI mtDNA barcoding, based on amplification of the mitochondrial cytochrome oxidase c subunit I fragment (Hebert et al, 2003a,b). Large data sets for many groups of animals have been published (e.g., Knebelsberger et al, 2014;Barco et al, 2016) and have been applied for rapid and reliable species identifications. However, this technique often demands taxa-specific optimization and several processing steps.…”