Molecular barcoding of north-east Atlantic deep-water sharks: species identification and application to fisheries management and conservation

Abstract

Two genera of elasmobranchii, Centrophorus and Centroscymnus, include species that represent the highest landings of deep-water sharks caught by fishing fleets operating in the north-east Atlantic. There are morphology-based identification problems among and within genera, and landings of processed shark products further prevent an objective assessment of these species. The present study is the first attempt to test the suitability of using a DNA barcode approach to discriminate accurately among the four most important commercial deep-water shark species: Centrophorus squamosus, Centrophorus granulosus, Centroscymnus coelolepis and, recently discovered in Portuguese ports, Centroscymnus owstoni. Sequence analyses of the mitochondrial DNA cytochrome c oxidase subunit I (COI) gene revealed low levels of haplotypic and genetic diversities. Higher levels of inter-specific relative to intra-specific divergences allowed discrimination among species, which form reciprocally monophyletic clades. Inclusion of published COI sequences from other species within the same genera revealed haplotype sharing among species, which calls into question the current taxonomy and accuracy of fisheries data available. Amplification of the COI gene coupled with MboI restriction digests was found to be a fast and inexpensive strategy to resolve within genera identification problems. Molecular barcoding constitutes a critical tool for the assessment and implementation of urgent management policies for this group of species.

A DNA Sequence–Based Approach To the Identification of Shark and Ray Species and Its Implications for Global Elasmobranch Diversity and Parasitology

“…The mean of the pairwise differences between specimens of C. granulosus and those of C. squamosus was 37.8. A similar lack of divergence between these two species was reported by Moura et al (2008).…”

“…The average of the pairwise differences between C. owstonii and C. coelolepis was 74.7 (or 7.15%). This result is somewhat more conservative than that of Moura et al (2008) who found the genetic divergence between these two species to be 12.8%.…”

“…There has been much recent interest in exploring elasmobranch sequence variation using the barcode marker cytochrome oxidase 1 (COI) (e.g., Holmes et al, 2009;Moura et al, 2008;Toffoli et al, 2008;Ward et al, 2005Ward et al, , 2008Ward et al, , 2009Wong et al, 2009;Zemlak et al, 2009). While such barcode work will provide a useful parallel assessment of sequence variation, the fragment of COI used is both shorter (650 vs. 1044 bp) and more slowly evolving in chondrichthyans than is the NADH2 fragment (Moore et al, 2011).…”

Genetic support for the morphological identification of larvae of Myctophidae, Gonostomatidae, Sternoptychidae and Phosichthyidae (Pisces) from the western Mediterranean

“…The identification of early life stages, such as larvae and transforming young, is essential for current studies on the distribution and reproductive strategies of pelagic fishes (Takeyama et al 2001, Moura et al 2008, Valdez-Moreno et al 2010. Thus, the assessment of biodiversity and its implication in the management of vulnerable marine ecosystems requires an accurate taxonomic assignment of fish larvae.…”

Skate-ing on thin ice: molecular ecology of longnose skates in the Southeast Pacific Ocean

“…In these cases, the amplified fragments from cox1 gene did not provided enough information to establish phylogenetic relationships in the species studied; mainly due to the use of technologies now considered obsolete, their inability to develop species-specific primers, and the inherent evolutionary close-proximity of longnose skates (Díaz de Astarloa et al, 2008;Naylor et al 2012a, b;Vargas-Caro et al, 2015, 2017. Sequences of all mitochondrial loci amplified in the present study showed over 98% identity and a low number of -82-based on morphology Moura et al, 2008;Toffoli et al, 2008;Ward et al, 2005Ward et al, , 2007Ward et al, , 2008Ward et al, , 2009Wong et al, 2009;Zemlak et al, 2009). Numerous studies have demonstrated the efficacy of using cox1 and nadh2 as diagnostic sequences for universal species identification in animal lineages, and the discordance between cox1 and nadh2 analysis was unexpected.…”