Genetic identification of Carcharhinus sharks from the southwest Atlantic Ocean (Chondrichthyes: Carcharhiniformes)

Abstract

Summary Sharks of the genus Carcharhinus exhibit subtle morphological differences that are difficult to observe because of the common practice of head and fin removal, making species identification challenging. A total of 317 sharks, commonly called ‘cação‐baia’ (large individuals) or ‘machote’ (small size) in Brazil, were captured by the tuna fleet at the Santos and Guarujá fishery ports on the southeastern coast of Brazil and identified at the species level by multiplex PCR. The Internal Transcribed Spacer 2 region of ribosomal DNA was amplified using universal primers, and species‐specific primers were used for some of the Carcharhinus species. A total of 313 shark carcasses were directly identified by multiplex PCR. Four carcass samples did not amplify; therefore, the partial COI sequences were used to confirm their taxonomic identity. The results show that more than one species was being traded under the same commercial designation, including some Carcharhinus species that are under protection by federal legislation. Such species misidentification directly affects the long‐term sustainability of sharks.

Genetic connectivity and phylogeography of the night shark (Carcharhinus signatus) in the western Atlantic Ocean: Implications for conservation management

“…Total genomic DNA was extracted from approximately 20 mg of the tissue samples using the DNAQIAmp Tissue kit (Qiagen Inc., Valencia, CA, USA). All the field species identification was confirmed by: (i) Multiplex PCR, as described in Domingues et al (); and (ii) using mitochondrial cytochrome c oxidase subunit I ( COI ) sequence data (Ward, Zemlak, Innes, Last, & Hebert, ).…”

“…Age at maturity is about 10 years for females and 8 years for males, with between four and 18 offspring being produced per litter (Ebert et al, 2013;Hazin et al, 2000). It is a severely overexploited shark species, being caught in pelagic longline fisheries targeting swordfish and tuna, mainly along the western Atlantic Ocean (Amorim, Arfelli, & Fagundes, 1998;Carlson, Cortes, Neer, McCandless, & Beerkircher, 2008;Domingues, Amorim, & Hilsdorf, 2013;Tavares & Arocha, 2008). Various characteristics of this species have been well studied in the western South Atlantic, such as fisheries (Domingues, Caltabellotta, & Amorim, 2016), reproduction (Hazin et al, 2000), age and growth (Santana & Lessa, 2004), demographic analysis (Santana, Duarte-Neto, & Lessa, 2009), and feeding habits (Vaske-Junior, Vooren, & Lessa, 2009).…”

Effects of the Pleistocene on the mitochondrial population genetic structure and demographic history of the silky shark (Carcharhinus falciformis) in the western Atlantic Ocean

“…Total genomic DNA was extracted from approximately 20 mg of tissue using the DNAQIAmp Tissue kit (Qiagen Inc., Valencia, CA, USA). To prevent morphological species misidentification from causing downstream interpretation errors, species identity of all samples was first confirmed using the multiplex Polymerase Chain Reaction (PCR) method in Domingues et al (2013).…”

Molecular identification of shark fins in Malaysian Borneo’s local markets

“…Various molecular approaches have been utilized in identifying shark species, including multiplex PCR and DNA barcoding (Hoelzel 2001;Shivji et al 2002;Holmes et al 2009;Wong et al 2009;Domingues et al 2013;Sembiring et al 2015). While using species-specific PCR primers, such as those presented by Abercrombie et al (2005), in the multiplexed PCR can facilitate identification of multiple species in a processed product, all the primers for all the species in samples must be available.…”