DNA barcoding of elasmobranchs from Indian Coast and its reliability in delineating geographically widespread specimens

Abstract

Identification of elasmobranchs by conventional taxonomy is difficult due to similarities in morphological characters. Species-specific molecular markers are good choice for identifying species irrespective of it's life stage. Recently, mitochondrial cytochrome c oxidase subunit I (COI) gene got global recognition as a barcode gene to discriminate all animals up-to species level. In this study, mitochondrial COI partial gene was used to develop DNA barcodes for 18 species of elasmobranchs (10 species of sharks and 8 species of rays). The COI barcodes clearly distinguished all the species with high interspecific distance values than intraspecific values. The average interspecific and intraspecific distance values are 8.6% and 0.3% for sharks, respectively and 12.4% and 0.63% for rays, respectively using K2P method. The Neighbor-Joining tree showed distinct clusters shared by the species of same genera. The COI barcodes were also used to estimate allopatric divergences for selected species across broad geographical locations and found that Sphyrna lewini, Aetobatus narinari and Neotrygon kuhlii have cryptic diversity.

Unveiling the molecular identity of the diminutive cyprinid, Horadandia brittani (Teleostei: Cyprinidae), a species endemic to Southern India

“…In our study, we examined the average nucleotide frequencies of the COI gene in four different species and found that A, T, C, and G content were 26.6%, 34.7%, 22.5%, and 16%, respectively, resulting in an average GC content of 38.6%. These ndings are consistent with previous studies that have reported variations in average GC-content in different sh species (Lakra et al, 2011;Pavan-Kumar et al, 2015;Bamaniya et al, 2016). These observations suggest that the variation in base composition can serve as a distinguishing characteristic to differentiate between different sh species.…”

“…Our study con rms these patterns of nucleotide changes, as we observed that most nucleotide (GC content) changes occurred at the third codon position (See Fig. 3), consistent with previous ndings in sh (Lakra et al, 2011;Bamaniya et al, 2016), as well as sharks and rays (Pavan- Kumar et al, 2015). Taken together, our results provide strong evidence that the COI gene can be effectively used to differentiate between species of sh based on these patterns of nucleotide changes.…”

Advancing DNA Barcoding to Elucidate Elasmobranch Biodiversity in Malaysian Waters

“…DNA barcoding—more specifically, CO1 analysis—has been used widely to aid in the species identification of elasmobranchs from various regions, such as Australia [ 36 , 42 , 43 ], China [ 44 ], the Philippines [ 50 ], Indonesia [ 51 ], Singapore [ 45 , 47 ], India [ 19 , 52 , 53 ], Bangladesh [ 54 ], Southern Africa [ 46 , 55 ], the United Kingdom [ 56 ], the Mediterranean Sea [ 57 ], the North Atlantic Ocean [ 58 ], the United States [ 49 ], and Brazil [ 59 , 60 , 61 ]. To date, limited published DNA barcoding studies in Malaysia have focused on rays but not on sharks [ 9 , 34 ].…”