DNA Barcoding and Species Delimitation for Dogfish Sharks Belonging to the Squalus Genus (Squaliformes: Squalidae)

Abstract

The Squalus genus comprises a group of small demersal sharks occurring circumglobally, popularly known as dogfish sharks. This genus exhibits a conserved morphology, thus making correct morphological identification difficult. Considering these taxonomic problems and the scarcity of molecular data, the present study aimed to identify Squalus genus MOTUs, using DNA barcoding for species delimitation via ABGD (automatic barcode gap discovery), PTP (Poisson tree process), and GMYC (general mixed Yule coalescent) employing the mitochondrial COI gene. A total of 69 sequences were generated from samples obtained from the American coast in both the Atlantic and Pacific Oceans. The ABGD analysis was the most conservative among the three applied delimitations, indicating three taxonomic units, while the PTP analysis revealed nine MOTUs, with two conflicting units noted between S. clarkae + S. mitsukurii and S. albicaudus + S. cubensis. The GMYC analysis indicated an excessive division, with S. acanthias and S. mitsukurii subdivided into six MOTUs each and S. blainville, into four. These findings demonstrated that Squalus presents a complex of previously defined species, with misidentified samples deposited in databases leading to difficulties in analyzing the real distribution and diversity of species belonging to this genus. Thus, further efforts to highlight possible new species are recommended.

I Like This New Me: Unravelling Population Structure of Mediterranean Electric Rays and Taxonomic Uncertainties within Torpediniformes

“…As concerns the quite divergent sequences retrieved in public repositories, obtained from specimens caught outside the Mediterranean Sea, they were analyzed using several species delimitation methods, recently applied to other elasmobranch species to address identification issues and solve taxonomic uncertainties [ 3 , 6 , 7 , 89 , 90 ].…”

Sharks - Past, Present and Future

“…Overall, sharks belonging to the Squalus genus exhibit conserved body morphology, making identification based entirely on morphological characters complicated, leading to misidentifications [110]. This complexity is amplified even similarly via the high overlap of morphological characters among species, as identification is often based on limited and insufficiently consistent characters, like the number of vertebrae and morphometric data [10,16,20,38,111,112]. In fact, morphological and biological similarities among squalids have led to considerable confusion over their taxonomy [14].…”

“…However, in a review of Japanese Squalus, S. blainville was defined as a species with high dorsal fins and long dorsal-fin spines [116]. The same review revealed that Squalus, referring to S. fernandinus and S. blainville by some authors, had short dorsal-fin spines and were more similar to S. mitsukurii from Japan, and suggested that nominal S. blainville from New Zealand could be identical to S. mitsukuri [112,117]. It was also noted that dogfish resembling S. mitsukurii occurred in Australia and New Zealand [31].…”

“…It was also noted that dogfish resembling S. mitsukurii occurred in Australia and New Zealand [31]. Outside its main distributional area (Mediterranean Sea and eastern Atlantic), S. blainville has also been recorded erroneously in Australia and New Zealand [112]. It was thought to be widespread in the Atlantic, Indian and Pacific Oceans [34,117] as well as in Japan [116].…”

Genetic Population Structure and Diversity of the Whitetail Dogfish Squalus albicaudus (Chondrichthyes, Squaliformes) along the Brazilian Coast as Identified by SNP Markers

“…Total DNA was extracted from 31 S. albicaudus samples obtained from individuals sampled from 3 different northeast and southeast Brazilian coast locations, namely Recife, in the state of Pernambuco (n = 14), Angra dos Reis, in the state of Rio de Janeiro (n = 4), and Santos, in the state of São Paulo (n = 13) (see Supplementary Figure S1). Fin and muscle samples preserved in 96% ethanol deposited at the Laboratory of Fish Biology and Genetics (LBP), UNESP, fish collection in Botucatu, SP, Brazil, were identified by the DNA barcode technique [46]. Due to the species demersal habits, captures are not frequent and most samples were obtained from local fishers and research collaborators.…”