The shark panel: An InDel multiplex for shark species identification

Abstract

A B S T R A C TThe Elasmobranchii comprises the diverse and important group of sharks and rays. The Selachii or sharks clade includes some of the ocean's largest predatory fishes, being commercially overexploited due to unsustainable fishing activities for their meat and fins. Overfishing has resulted in significant population declines and several Selachii species are now considered under high threat and facing extinction, with about 93% of its nominal species included in the IUCN Red List. Molecular data has provided important information about these species, allowing the management of natural stocks and their decline. Population genetics, connectivity data, and their population genetics knowledge are now available and play an important role on establishing conservation policies. However, despite the ecological, commercial and conservation importance, no molecular method is available to identify sharks in a forensic analytic context. As a first step in the construction of a reliable method for shark identification, we carried out a molecular systematic analysis using 85 previously published mitochondrial 16S rRNA gene sequences obtained from the NCBI database. We found that indels in the 16S rRNA gene can be used to distinguish almost all the analyzed shark species, including some of the most threatened according to IUCN Red List. The regions selected in this study can be used for the construction of molecular assays for shark identification in a forensic context.

Probing the potential of the Shark Panel InDel multiplex v2.0 on the forensic identification of batoid elasmobranchs

“…Mainly relying on DNA barcoding methods for molecular identification, both researchers and law enforcement authorities still struggle when dealing with taxonomic uncertainties and fragmented/processed material. In this sense, trying to fill this gap and following the path for the Selachii species studied by [6], five hypervariable InDel regions were defined for the development of primers and now are being tested for several elasmobranch species including sharks and batoids.…”

“…Following the development of the Shark Panel v1.0 [6], which includes uniquely sharks, now we tested the effectiveness of the v2.0 multiplex on batoid elasmobranchs. As for the first version of the multiplex, aiming the construction of a reliable method for batoid elasmobranchs identification, we carried out a molecular systematic analysis using previously published mitochondrial 16S rRNA gene sequences obtained from the NCBI database.…”

Probing the potential of InDel polymorphisms on the molecular identification of cetaceans

“…Recent studies have proved that this methodology is appropriate for molecular assays and have been used for other marine species identification [20,21], but there are no specific assays for cetaceans in this area. In addition, the affordance of this kind of identification without needing of sequencing, only performing electrophoresis capillary for determination of fragment size [8,18,22], must enable newa protocols.…”

Shark Finning and the Molecular Identification of Shark Species: Review and Perspectives

“…Methods such as protein electrophoresis [41,[44][45][46], restriction length polymorphisms (RFLPs) [39,42], PCR methods [40,[47][48][49][50][51][52][53], species identification using insertion-deletion regions (indels) [54], and the nucleotide sequencing approaches mainly focused on mitochondrial genes and commonly using the DNA barcoding methodology, such as presented by several studies [55][56][57][58][59][60][61][62][63][64][65][66][67][68][69][70]. Pank et al…”

“…This approach was recently applied to shark species identification by [54] that used indel regions from the mitochondrial 16S rRNA on the identification of shark species, including several figured on the IUCN Red List, and also included between the most prevalent species targeted by the shark finning industries. As presented by Carneiro et al…”